My mare is starting to really round and lift herself, which is awesome, but I am starting to have a really hard time sitting her much bouncier trot, especially now that my instructor is starting to have me work on trot extensions. Any suggestions for how to help me sit better? Right now I feel like I am really bracing against my stirrups, which makes me feel like I am sitting in the downward motion of the trot really hard, which can’t feel too good for my pony.
You answered your own question: “I feel like I am really bracing against my stirrups,” In other words, ride sitting trot without your stirrups (collected and working trot). Then when you feel like you are really sitting it well, begin by lengthening the trot a little at a time until you are used to how your legs need to assist you in your balance and moving with the trot. You could even get your instructor to put you on the lunge line for some of this work. As the punchline to the old Carnegie Hall joke says, “Practice, man, practice!” 
You simply cannot grip with your legs. This is about core strength and flexibility in your hips and back. How fit are you? This type of riding requires real fitness, the more time working on your own fitness, the better the results in the saddle.
I also highly recommend work on the lunge line.
Also, never spend a lot of time sitting poorly. Practice doesn’t improve us, correct practice improves us.
Go back to sitting the working trot. Be honest with yourself. Are you grippy? Do you really follow the motion? If the answer is “yes” to these then start doing transitions within trot…working to medium to working. Only stay in medium a few steps until you can sit medium as well as working.
When you are 100% at the medium, start adding a few extensions.
Again, work on the lunge is priceless. Especially with your eyes closed. Your body instinctively sits more deeply and moves better with the horse this way.
And, as they say, Rome wasn’t built in a day. Be patient with yourself.
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Thinking about allowing room for my horses to lift into the larger gaits has been the #1 help for me riding them. My mare now goes into medium if I essentially think of raising my ears (as my head would be lifted by a string if I were a puppet, a famous comparison.) I can feel it even sitting in a chair at lunch now - my spine becomes straight instead of my typical too arched back, pelvis goes to neutral, and my seat just feels lighter on the chair. Because I’m SUPER short waisted, it also lifts my ribs enough so they don’t overlap with my pelvis which allows me room to move with my horses.
My gelding had a VERY hard to sit trot, and in his case really increasing swing through his back has been monumental in making a difference. For him, I found I could sit the trot immediately after cantering, so I started asking for lengthening from there instead of from a trot, and it really helped me not grip and sit properly. In his case, our size mismatch means I really try to grip instinctively and have had to untrain that reaction. On a longe, he goes flying into an extended trot as soon as I lift my legs up and completely off him - and I can sit it until I laugh too hard that I start bouncing. It’s kind of a joyous feel from him and I would dare anyone not to find themselves in gleeful laughter when they feel it. 
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Two suggestions. First, I really like my acavallo gel half pad. It really helped my sitting trot.
Second, if you are bracing in the stirrups you are pushing yourself up out fo the saddle. Be sure your weight goes down into your heels with a flexible ankle. Start with a small but active trot. You will find it.
^^^ This. Especially the core strength. To me it sounds (might be wrong because I have no idea how you ride) like you do still have something missing sitting a good trot with suspension. And yes it about fitness, but it is also about technique. and the most important moment is the transition into trot… You kind of need to feel like you suck yourself into the saddle.
I’m older than the hills and so is my horse, so we don’t do much ambitious trotting anymore. Add up our ages and we are 92. My right hip and knee don’t want to post, so I started sitting. Another better rider asked me one day how I made it work, so I actually thought about it. I have an image to keep my legs off the horse and let them float. I feel lower in the saddle and can follow him, and we are working on developing more energy without my banging on his back. If I push on the stirrups, it all falls apart.
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SOmething to add to my post above - sometimes the saddle is an issue. I had a saddle that was checked by a reputable fitter and it did fit me and my horse - but I could NOT sit his trot. Then I had an epiphany on the
lunge line - I was sitting slightly angled on the saddle… right hip back. Spoke to fitter and she mentioned that sometimes a slightly too wide twist will do that - note the saddle I had was NOT known as having a “wide” twist - So she came out and I tried a different saddle and like magic everything was better…
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Remember that if in your efforts to send forward you tighten your grip on the reins. her head will come up, making sitting much harder. Remember to give forward while still maintaining the contact you need to allow her head and neck to come a little forward, which is necessary in lengthening and extensions.
It might not be your inability to sit but that she stopped giving you her back, because she elevated her neck
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I found this article on the Dressage Today website and remembered reading your post. I found it helpful/interesting, not sure if you will or not, but thought I would share none-the-less…
https://dressagetoday.com/instruction/how-build-core-stability-in-the-saddle-without-becoming-stiff
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I’m nowhere near ready for extensions but this! getting the correct for me saddle that helped my hips be in the right position made a world of difference.
The OP is not doing extended trot but merely lenghtening it, which should be part of any good training ride.
The ability to lenghten and shorthen the strides, at all gaits, will also help the rider finding and stabilizing his position in the saddle.
To the OP; Short sessions of sitting and rising trot are the best in order to learn and build the right core muscles for both you and your horse.
Also, I wouldn’t start sitting the lenghtenings as of now since you have trouble sitting it through properly. Your mare might not be yet strong enough in her back for that. That’s why first level doesn’t require the sitting trot no more, too many horses were not physically ready for it.
Like for the stretchy circle, which is asked to be done in rising trot for the same purpose, lenghtening of strides also implies lengthening of the whole frame/top line. Rising is, at the beginning, the best way to ensure proper carriage and throughness.
The sitting trot shouldn’t be rushed, it’s fun but it really does have an impact on the horse’s way of going.
Better for rider to develop a good, active and precise rising trot.
You have had lots of good advice and tips here. From my own personal experiences I have found that working on my core fitness as well as riding regularly with a clinician with a solid understanding of rider biomechanics has been incredibly helpful. It sounds like you already have good body awareness to know you are bracing in the stirrups and might find it useful to read books or watch videos by a biomechanics expert Mary Wanless.
Sit like you are advancing a pogo stick.
