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into the schedule, might I suggest you're overdoing the "schedule"?!
Hell we had trouble fitting "school" into all the darn activities we did! Kung fu, swim team, gymnastics, dance, soccer, baseball, track . . .
Keep 'em busy and keep 'em tired! That's my motto! 
Seriously, don't try and "have school all day" - where's the fun in that? If you're just "doing school at home" - you're truly missing the whole point - and the best part - of hs'ing. Which is FREEDOM!
Freedom to study what you want, when you want, HOW you want, where you want.
School in jammies in front of the fireplace? Fine.
School at the park? GREAT!
School at the local museum? Fantastic!
School with your friends at their house - all the better if you get a little free time.
Co-ops are wonderful inventions.
We used to joke that we "car-schooled" since we were always going places and that's where he did a lot of his "paperwork". We also did a whole lot of discussion in the car.
Not trying to be all bossy or anything, but if you're new to hs'ing, you're probably trying to recreate "school at home" - we all did that. Throw of the fetters and go outside! Run around, be crazy, look at things, talk about things, explore and have adventures. THAT's homeschooling at it's finest.
Actually there is a lot of overlap but I think of gym as mostly body conditioning and PE as encompassing much more, like balance and dexterity.
Lately we've been using something called a Trikke which requires a lot of mental effort to make work, like roller blading or ice-skating, except I think it's more whole-body.
Also, Yoga and stretching come to mind.
As to how to fit it into the schedule, I can't help you there except to point out that it might be easy to fit it in where there's room, evenings weekends or even as a reward for completing other more academic work...
