[quote name='farley91']How do you know if GBA games come with the box and manual? All the GS around me just have the carts in the case. Do you have to ask if they have the box and manual? Sorry I don't know this as I never bought a used GBA game from them before. A GS near me has both Summon Nights and I would like to pick them up if I know there is a chance they could have the box and manual.[/QUOTE]
The great majority of stores threw out GBA boxes to save on shelf space. The store where I found boxed games had them in a glass case that was part of the side of their wraparound counter, versus most other stores where the games are locked in a sort of vertical case somewhere on the salesfloor. The only way to really tell if they still have boxes is to give the store a call. Looks like you already know what store has what you're looking for, so that should save you time from unnecessary calling.
Personally, when I was hunting for a boxed copy of Yggdra Union, I just looked at the store locator and call the ones that had the game. Before I made them confirm that they had the game, I asked them if they still had any GBA games with boxes. They all responded that they did indeed throw them out, so I said "thanks anyway" and frowned. Ultimately I decided to just drop an extra $17-ish dollars for a complete but open copy from eBay.