It won't hurt to flash as much as you want. Be sure to flash, at least, dalvik cache with each flash, and preferably also wipe factory data (from Recovery) before you do.
Apps 2 SD hasn't been explored too much on Eris yet. My understanding is that you have to create a partition on your SD card for it (back up everything on your SD card to your computer, first!).
It's on the EvilEris ROM because the EvilEris ROM is based on the Hero's VillianROM, which has it built in.
I always create a nand BACKUP (boot to recovery, hit backup/restore, nand backup) whenever I am going to flash a new ROM, just in case it doesn't work.
when you go back into recovery at some point (any time) later on, you can go to backup/restore, and do a nand restore, and it restores EVERYTHING, your apps, your contacts, your screens, your icons, EXACTLY how it was when you did the nand backup.
So flash all you want. just do a backup first (I recommend) and make sure that, AFTER you do your nand backup, you do a data and dalvik cache wipe, all from recovery, before you flash a new ROM