Some very good advice here!
Remember, one of the essential basic skills of baseball is baserunning. So, you can get some conditioning in while running bases. They won't even know its conditioning.
I would suggest during BP making one of your stations baserunning (ie, 3 min @ 1st, 3 min @ 2nd, & 3 min @ 3rd), or better yet, spending the last 15-20 min. of practice running bases.
We frequently use this routine:
1. Home to first, look over right shoulder for bad throw (return to home).
2. Home to first with narrow turn, back to 1st (return home).
3. Home to second with wide turn.
*Narrow turn=visualize running out a ground ball that makes it through the infield for a hit. The turn is later than wide turn and shaped like a question mark. Wide turn=visualize a double laced in the gap-shaped like a banana.
4. First to second-steal with batter taking/manager acts as pitcher (return to first).
5. First to second-steal w/o take (return to first).
*Coach near plate simulates fly ball/pop up by pointing up, line drive by pointing level, and ground ball by pointing down. Hitters look in to "read" the batted ball.
6. First to third using third base coach.
7. Second to third stealing on one-looker (return to second).
8. Second and round third with third base coach holding runner up (return to 2nd).
9. Second to home.
10. Third to home-squeeze (safety or suicide)return to third.
11. Third to home-tagging up/manager in outfield simulating OF making catch by slapping bare hand in glove.
12. Reading down angle and scoring on wild pitch/passed ball.
Whenever possible in this drill we use two throw-down bases and have three runners going at once (#'s 4,5,7,10,11,&12).