How did you maintain your fitness while underway?

You have to find the time when you can. Between watch standing, Rating/ESWS quals, drills, meetings for drills if on CSTT or DCTT teams, ship all hands evolutions and collateral duties, time is at a premium with 20+ hr days the norm. I worked out whenever i could, whether it was 0300 or 1300. Small boys usually had some universal weight sets, some free weights, treadmills and stationary bikes stuck in every nook and cranny of fan rooms.
PO1 Andrew Gardiner gave you some really good info.

I made time. After working a schedule of how my department would do admin and watch, I worked a way to incorporate a 2 hr workout into the mix. The only deviation I would allow would be if my body was waaaay to tired or that I was feeling under the weather. My workout was intense but I loved working out everyday.....I also would be climbing ladderwells all day to get from point A to point B; so I got a workout everywhere I went.

I was on LSD's and LHA's. We ran a lot, up and down those damn steel ramps. We even dawned full gear, packs and weapons and humped around the flight deck and ramps for an hour. My shins never hurt so bad. We also never used mats like you see in the photo.