I have recently started collecting comics hardcore. I've bought a few local collections, traded some and got myself a nice little collection of new and vintage books. What I'm wondering is other then boarding and bagging my comics, what is the best way to store them? Boxes? Bins? I want to know what is the best way to go and when it comes to highend/rare comics what's the best way to protect them other then a board and bag, and getting it graded as that's too expensive for more then 1 or 2.

I think the best way to protect your collection of comics is going for boxes. Preserving expensive ones are important and you need to put the box at the right place in order to avoid moisture and insects if you can't afford to lose them.

At the moment, every single comic I own is boarded and bagged. Majority of my collection is only worth the cover price or less/slightly more. But I do have some vintage stuff and recently got the first appearance of Deadpool, so I want to make sure they are protected. I'm thinking of getting the Deadpool comic graded. I have them all on a bookshelf off the floor, away from sunlight and aside from being climate controlled have them stored as best I can.

I have that comic New Mutants 98# or something like that, although mine's in ok condition, been tempted to offload some of those. I also have first appearance Gambit as well which is in better condition.

Boarded, bagged, and boxed. I have all mine like that.
Note of caution however..! Many years ago, I bought some comics that had the bag scotch taped on the flap. I would absolutely remove the tape, and don't think about doing that. I was pulling a golden age comic out of the bag one day to look at it, and the tape partially stuck on the cover on the way out. It ended up taking off part of the cover. My 10 cent "Crime Does Not Pay" comic was basically ruined.

I haven't collected comics in years, so I'm not up-to-date on the latest in pulp-literature conservation. When I was a teen in the 90's, my father and I were heavily into comics and we had around 20 boxes stuffed to the brim of comics, mostly Spidey, X-Men, and a few others. We had all comics bagged and boarded, and one thing our seller recommended was to get silica dehumidifying packets and keep in the box. Temperature & humidity changes through the years can cause warping or mildew, so the silica packets help to curb that chance.

Acid free bags and halfback boards for your standard stuff. BCW or other standard brands are fine.
Mylite 2's and fullbacks for your hardcore investment books. Gerber is the way to go with these.
If you can't afford fullbacks, buy silver age mylar and silver age backerboards. Double up the acid free backing boards at two per book for rigidity.

Normal comic boxes, long or short for standard storage.
Magazine box for your investment books that are stored in the fullbacks or in doubled up silver age boards.
BCW Plastic Tote for transport if you are taking them somewhere.

Microchamber paper your gold, silver and bronze age books that are worth something. If you buy backer boards that are coated on one side, then put them in the bag with the shiny, slick side touching the comic.
As webz mentions above, there's nothing wrong with a silica packet in your cardboard storage boxes, but that is more effective at resolving moisture to keep silver tails out of your boxes than it is at doing anything for the comics. The backerboard should handle any acid residue that is catalyzed by ambient moisture. If you have more moisture than that in storage then something else is wrong. Moisture issues on comics was widely resolved on a broad scale by bag and board storage.

BCW storage boxes, with BCW bags and boards. I swear by the stuff