The updater/launcher won't touch original THUG2 files, so replace decks/griptapes in THUG2's directory and you're fine. As for backups, going to be blunt but it's really a personal problem if the user doesn't bother to do it, but regardless, I'm sure plenty of people would be willing to send a copy of lost files. Or host them on Mediafire etc.
A con for using img files is the extra steps in saving and converting your graphic, but if you're doing one or two graphics it's not bad.
If you want to use the game's native format, you'll need these tools:
http://www.mediafire.com/file/uyhphyb8bn4gefc/THUG2+Texture+Tools+by+defeat0r.7zDeck graphics and griptapes are stored in "Tony Hawk's Underground 2\Game\Data\textures\Boards". Use IMG2TGA to convert the img.xbx file. You can rescale to whatever size you want (I've used up to 8x vanilla size for the entire set of griptapes, THUG2 engine is surprisingly flexible), just keep the dimensions a power of 2. The important thing to remember is when you're ready to save your graphic:
Convert to indexed image, then convert back to RGB, and then save without RLE Compression. I use GIMP, which has the options for that under Image > Mode. No idea for Photoshop or Paint.net. I should get with someone who uses those and write a comprehensive guide on this stuff, Texmod method included too.
Then when you drag your new file into TGA2IMG, type "y" for compression when it asks you. Should convert and there you go, just replace whatever file in vanilla THUG2 and you'll see your new one. Of course, only you'll see it online. Others will see what graphic you replaced.