When going from Safestrap to Bootstrap it's very easy:
1. Make sure you're in "non-safe mode" and boot up to the ROM
2. Open up Safestrap.apk and click the "Remove Recovery" button
3. Go into Settings -> Applications and remove Safestrap
4. Now you can install Bootstrap like normal
Going from Bootstrap to Safestrap *should* be just as simple, but for some reason there are occasional hiccups which can be solved by starting off with a stock system (+ root):
1. Remove the Bootstrap apk by going to Settings -> Applications (there is no "Remove" inside the app)
2. Install Safestrap.apk
3. Click the "Install Recovery" button and double check that you see the 1.06 in the lower left corner.
DO NOT ATTEMPT TO MIX AND MATCH BACKUPS FROM 2 DIFFERENT PROGRAMS. If you made the backup in Bootstrap then you can recovery with it in Bootstrap. Same goes for Safestrap. They are in different directories now on the SD card so it shouldn't happen, but it bears repeating.
If you have error messages on the installation:
1. Make sure you have root
2. Make sure you have about 3 megs free on your system drive
3. Make sure you're up-to-date w/ Superuser.apk and have rebooted at least once after upgrading.
4. Make sure you have a decent version of busybox installed
The main benefit of Safestrap over Bootstrap is the ability to ALWAYS get back to recovery by never directly clobbering your main system partition.
Some cliffs notes for Safestrap:
1. It uses the /preinstall partition as a 2nd-system partition to boot a 2nd ROM from.
2. So, anywhere in the recovery where it mentions "system", it's really talking about your preinstall. This is true for non-safe mode OR safe mode.
3. All features like "format /system" and flashing ROMs while in Safestrap only affect /preinstall and not your original system. This is true for non-safe mode OR safe mode.
4. There are 2 "modes" for Safestrap: "non-safe mode" where you boot up to your original ROM from the primary system partition, and "safe mode" where you boot from the /preinstall partition (2nd-system).
5. When you choose to change modes via the Safestrap Menu -> Toggle. The program takes your current /data and stashes it in a data file. Then checks for a saved data file from the mode that you're going to and restores it.
6. Don't ever use the "QUICK" (Unsafe) Toggle. Unless you're "stuck" in Safe Mode and getting an error when trying to swap back to non-safe mode. This QUICK toggle skips the saving of your current /data and the restore of your saved /data from your main ROM. It's meant as an emergency exit. You will need to restore your original ROM /data from a backup made while in non-safe mode.
7. Treat backups made in each mode as separate. Because "/system" will be whatever you have on your 2nd-system at the time, and /data is which ever ROM is active. While in "non-safe" mode backups automatically include the original system partition for disaster recovery. Backups made in "safe mode" give you the option of backing up the original system.
Good luck.
From a personal stand-point, where I dev at odd hours of the day and night, it's unbelievably handy to be able to swap to ICS for an hour and dev on it, then swap back to whatever stable ROM I'm running on my primary system so I can answer calls and use my phone .. as a phone.
