Help for "Safe mode"?

[Catnap]

According to the SD User's Guide " It’s usually a good practice to quit all running applications before performing a backup. Since there are some that aren’t visible, like the Microsoft Office Database Daemon, it’s easiest to log out of your account, and then log back in with the Shift key held down. This will prevent your startup items from running" and I want to make a bootable clone before I start doing a system upgrade. If I can make a valid clone without being in Safe Mode, then I don't need Safe Mode. But I do have Microsoft Office installed.

Could Unsanity's APE (Application Enhancer) be involved here? I know I need to turn it off for really big system updates. If I turn it off before cloning, can I turn it on again from the clone when (if) I'm running from the clone?

If I can clone without having to be in Safe Mode, I'll be happy. Thanks for your time.