From what I can tellâ€"unless I am wrong on thisâ€"the only way you can manually specify the import resolution (i.e. the "Import at 640X480" checkbox) for sprites is when you import them individually. When you try to import multiple sprites or import from an animated GIF, it assumes that you want to import them at 640X480.
I need to import things at 320X240, and as a consequence am having to export all frames as single files from Photoshop and then re-import them one by one -- what a pain! It'd be nice if I got a little checkbox like that on ALL sprite importing options.
(For those who care, my game is actually set to run at 640X480 but it's really a 320X240 game. I run Windows in an emulator that doesn't support 320X240 resolution, so I have to double it and have it automatically scale things up. If I mistakenly import at 640X480 then I get tiny sprites. Boo hoo, what a sob story, I know, but anyway, it'd be nice if that option was just made universally click-able.)
You can always resort to tiled sprite import. Not as comfortable, but quicker than doing it one by one.
Actually in your case it would probably be better to develop the game in 320x240 resoltion and force 640x480 through winsetup.exe when testing/running the game. The current way you'll have to import scaled lo-res background artwork, and despite compression it may take up more space than true 320x240 images.
Yeah, as GarageGothic says, don't change your game's resolution just because of your graphics card. Far better to develop it properly at 320x240 and then adjust the settings in Winsetup so that you run it at 640x480.