Ok, so I've bought two copies of the game, one standard edition from Amazon (Borg BO Whoo-Hoo!) and one Collectors edition from Gamestop (Red Matter Capacitor, TNG Uniform, DS9 Uniform, Plus a pre-refit Constitution Class Light Cruiser Starting ship? Oh HELL YES!).

But while I've already input my pre-order code from Gamestop in, bought my lifetime sub (pays for itself in two years, I probably won't even have hit the level cap by then, easy economic decision) but, I'm seeing a lot of things here in the forums and on the site talking about inputting your keys as early as possible, the key from my standard edition from Amazon will be in the Game box itself, and estimated delivery is the 10th, is there some kind of time limit to when I can input the key?

Nope, no time limit. You can input the key whenever to get your bonus.

The only time limit is on how long the head start "grace period" lasts - if you do not start a "normal" account by Feb. 6th, you won't be able to log in until you put at least one retail key into your account. Preorder bonus codes are forever, though.