Personally, I store my cards in a combination of sleeves, toploaders, and binders. I keep a set of all C/U/R in a binder (with duplicate Rs stored in the back for protection purposes), and RR/SR/UR cards in sleeves and toploaders. Duplicate U/C cards are stored in storage boxes or tins. It's not particular expensive, but I'm not really a big-time collector or anything.
If you're looking to collect complete sets, buying 1 booster box and filling out the rest with singles/trading is probably your best bet. For English, anyway; if you're going Japanese, I'd suggest 2-3 booster boxes because the boxes are smaller and the pull rates are better. The biggest problem with English booster boxes is that they're so swingy in terms of pulls, so you might end up with a large amount of EX/FA cards... or you might not. But getting one box will at least give you a full C/U/non-holo R set and some wiggle room for everything. The more boxes you buy, the more you'll be gambling on good pulls for those EX/FA cards, so it's up to you if you would want to be that risky about it.
Picking a set is more or less a personal choice if you're planning to collect and not play. Older sets (such as the beginning of the XY block) are already going out of print, so if you're planning on buying a box it might be a good idea to snag those before they go up in price much. Otherwise, I would pick whichever sets interest you the most.
If you don't plan on keeping your dupe C/U cards, you can probably sell/trade them as bulk to people or resellers who do want bulk. There are a few traders on PB who accept bulk cards for trade, which might be a good way to get some cards that you're missing.
If you'd like a checklist to keep track of your collection, I'd suggest checking out
this thread, which may have some useful resources for you.
Good luck and have fun!
