Are you ready for those magic words...
"It depends..."
First and foremost, how much time do you have? That will dictate a lot of what you're able to do.
In terms of volume, that's not an easy one to answer. It really depends on how well the kids are recovering. If they show up to practice the next day and the entire team is really dragging, the training day before must've been too much. With that said, it may not have been the conditioning, it may have been the skill training itself. Unfortunately, there's no magic number of sets and reps. It's unfortunately a big game of trial and error and ultimately experience is going to be your best guide.
In general terms, you can do a higher volume when the intensity of the exercise is low. So, if you're doing a push-up, that's a pretty low intensity exercise and you can do a higher total volume. Now, when I am talking about volume, that doesn't mean doing 3 sets of 20. If you want to get in 60 reps for that day, you can still accomplish that by doing 10 sets of 6. Here's the difference...the 3 x 20 is working for one physiological attribute while the 10 x 6 is working for another. 3 x 20 is working on primarily muscular endurance and potentially hypertrophy depending upon how you're performing the exercise and the loading. In contrast, 10 x 6 is working more muscular strength and very slight hypertrophy - which isn't always a bad thing as it helps to modify body composition and with female athletes, unless they're injecting steroids, they won't get too bulky. So, what is the goal? Muscular endurance, muscular strength, power? That's going to dictate your individual set/rep schemes. And, in terms of volume, again look at the goal as well as the intensity of the exercise.
If you want pure strength, you can't obtain pure strength by doing a set of 10. When I work pure strength, I'm lifting very heavy loads and I'm doing 10 x 1, 8 x 2, 6 x 3, 8 x 3, etc. It's no different in gymnastics conditioning. For example, if a kid can barely do a pull-up - well, that's pretty much a maximal effort. So, if you want to build strength, don't ask them to do 20 in a row. If you want a high volume and 20 total reps, then have them do a total of 20...since the gymnast can barely make one...have them do a single pull-up 20 times with adequate rest in between. For a maximal effort exercise, they should rest at least a couple minutes as this not only allows the muscles to recover, but also the central nervous system. Most folks don't recognize the importance of the central nervous system and CNS fatigue. When it gets tired, it will not conduct the nerve impulses as rapidly or as frequently.
As far as how to run the conditioning, I've done it both ways - event, general, and combination of general and event conditioning. The more and more that I observe how folks in the world of strength training, power lifting, and Olympic lifting do things, I think in the future I'll probably as one of two ways...
I'll either set it up as 2 2-day splits between upper and lower body and include both general conditioning exercises (push-ups, pull-ups, etc.) and sport-specific exercises (planches, cast handstands, drop kips, etc.). One day will be for maximal effort work while the other will be a speed day where my only focus will be on doing exercises really fast (still with good form, though) so as to work on increasing the rate of force development. In other words, this is neural training to get the muscles to turn on faster and to attain more efficient muscle fiber recruitment.
The other idea that I'd consider is to have full body workouts with one day being for general conditioning and the other being event specific with some exercises for speed mixed in. Always put the speed or power (plyo) work at the beginning because you want the kids fully rested so that you can obtain maximal output. Even if you strength train after, it shouldn't make them that fatigued. In fact, many believe that it sort of gets the motor units "turned on" even better through a phenomenon called postactivation potentiation. If this doesn't make sense, go "Google" that term. You should find some info.
To answer the "early in practice vs. the end" - again, it depends. Where are you at in your season? Are routines the most critical thing? Then, put it at the end with the goal being two-fold - a) maintenance and b) injury prevention. Are you in the summer - then, put it early as you will probably be more focused on building strength and ultimately developing that into strength endurance & power as you sort of shift to a pre-season mode (6-8 weeks from first meet).
The "pyramid" approach is for bodybuilding. You aren't training bodybuilders and even if you were, again, females don't have the hormones unless you've supplying them with steroids. Even the "beefy" kids won't bulk too much beyond where they might've already been due to their genetics.
There's a million different ways to do this and gymnastics is so hard to train for because of the demands of the sport skill training. Recovery is the most difficult part of any strength program. The body has to have rest time. It won't adapt if you just keep beating it down. Another thing to keep in mind is the idea of adaptation - cycle your exercises every 3-5 weeks as the body does adapt rather quickly and you must change the stimulus on a regular basis.
While I'm on my soapbox, I'd also recommend doing less crunches and sit-ups for your core work. Do more planks, hollow holds, levers, side planks, woodchops, resisted rotation, etc. The core was designed to stabilize and transfer force - not be a prime mover for forward flexion. Also, teach your gymnasts to stabilize the core on skills such as front handsprings and to extend the hips by squeezing their glutes (butt) as opposed to hyperextending the spine.
Good Luck. Hopefully, this gives you a few new ways of thinking about how to approach strength training for gymnastics.