Tenax, thanks for the patience- with so many threads it's easy to lose track of some that I could and should answer - bumping it today brought it to my attention. Welcome to the forum - comming here and following the advice given will save you unbelievable amounts of time, $ and frustration.
The company I work for installs 40 - 50 IG liner pools/ yr, all of them have timers, though none of them have leaks in the system. The best thing to do is fix all the leaks, the easiest thing to do is to put a check (or backflow prevention) valve immediately in front of the pump inlet [if you do this put a union on the pool side of the check valve - you'll thank me every fall when you go to close the pool - also oversize the check valve , if the pipe is 1 1/2" use a 2" valve, they reduce flow and oversizing can alieviate that quite a bit]
As for the aquarite, when we install one it has a constant power supply, the unit can not turn on without the pump running and having it powered intermittently I believe is bad for it's 'computer' (you can check with Goldline/ Hayward but sometimes getting a straight answer from them is an exercise in futility, though the tech support is quite good)
As for your last ? - I would always recommend using bleach over the 'superchlorinate' function, because the cell's life is a direct result of how long it generates - a few bottles of bleach are a lot less expensive than a new cell! (If you can find the proper 1/2 unions (the male ends), making a 'cell replacement' sounds like a very good idea for swamp [I mean Spring] clean-up. Hope this was worth the wait, if you've any more ?s - ask away and you will be answered-- Have fun with the pool!!!