if you use auto installer, it just puts a folder named /and/ in internal memory (MyDocs) and if you use 2gb external micro sd card (suggestion: use class 6 or class 10 for best results), it just put those file on the card, in both the cases it doesnt erase your files until you reflash with custom emmc or full flash (rootfs and emmc both).

I must strongly recommend you to install Backup-Menu app from extra-devel repos and create a backup (just restart n900 with keyboard out and follow the instructions) in order to save your settings and installed programs before you install NITDROID