My method for what they're worth...
In general - load as soon as purchased. i.e. Unless it is a time limited offer (like the OM GC deal) I only buy what I can unload that day or so. Once confirmed as unloaded the card gets marked with a sharpie to show empty, date and where it went.

I keep a spreadsheet with tabs for;
Prepaid: Balance for each card, last reload date and next possible reload date (tells me how much float I'm accumulating and need to cash out)
All credit cards - app date, time between apps, sign-on bonus, requirements, bonus categories and accumulated spend etc.
Prepaid load dates - for things with a rolling clock for loads so I know when I can next load.
Cashback tracking - for things like TCB / UR mall purchases
Earnings rate worksheet - to track what different methods actually cost (i.e. $3 per $1k load at Target, $3+$1.25 / $400 ATM etc.)
In general I don't like to keep a balance over $3k on any one card and will pay it off well before the due date, sometimes multiple times a month. (I get paranoid about carrying too large a float and screwing up, so I work as hard if not harder at emptying the float as I do mfg spend).

I also use Mint to track total spending. You can connect most accounts (pretty much all the AMEX prepaid variants, even Paypal - but not GoBank).
I edit the spend category to 'transfer between accounts' for things like gift cards and VR and split the transaction to assign 'frequent flyer spend' to the portion that is the actual cost. So in the Target example where the load is $1,003 this shows as $1k transfer between accounts and $3 as FF spend. Costco ATM would be $400 transfer, $3 and $1.25 as FF.
Doing it this way allows me to separate my regular spend from mfg spend and allows a running tally of what this hobby is actually costing me. The 'transfer between accounts' category doesn't track as spending which would mess up any budgets you have if you don't use this approach. When I get say a TCB payout I also apply the FF spend category which then shows as a reduction in my FF spending. Same goes if I get a payout from selling gift cards or similar.