Welcome to TFK, I hope I can help you a bit your new filter should be enough for the tank with out using either of the others, the aquaclear 50 is capable of 200 gph (according to a vendor website) which should be fine plus maybe a little overkill. Not knowing your experience I have to ask if you do know about cycling your tank? If not a good read is here http://www.tropicalfishkeeping.com/f...m-cycle-38617/
You have done the correct thing by moving the filter over from your already established tank which will seed the new cycle, but it is probably important to keep it going all of the day because the bacteria you have built up in it will die with out a source of ammonia, I'm not sure if you meant the filter from your 5 gallon runs all the time, or just during the day?
You don't have to run both the filters to seed the tank, you can take the filter cartridge from the filter from your 5 gallon and put it in the new big one, or if it doesn't fit you can just leave the filter cartridge in the tank next to the inlet of your new filter.
I hope this helps you a little.