I'm very sorry to hear about the theft. I hope you will be able to get your computer back!
I am glad the article was of help! FileVault essentially turns your "Home" directory into a "safe zone" that is encrypted on disk. As such, you are free to place any files you wish on an external drive or on a non-encrypted location of your internal drive (pretty much anywhere, in fact) while you work on them, then copy them back into the vault like you would do any other file. You are right in remembering to use the Securely Empty Trash command to delete the file from the non-vaulted location as a simple Empty Trash would defeat the purpose.
You can definitely enable FileVault at any point you wish, provided you have ample free space on your drive – at least as much free space as your home folder occupies space on the drive plus a "good deal" (to your discretion) of padding. Note however that some stray files may remain on the drive.
The safest procedure would be to:
1. Backup all your files
2. Boot from the Mac OS X install DVD
3. Secure Erase your hard drive (7 Pass probably)
4. Partition the drive, install Mac OS X as usual skipping the migration assistant
5. Enable encrypted memory and FileVault using the secure delete option
6. Update Mac OS X
7. Install and update your apps
8. Only then migrate your data back
A lot of work indeed… Then, peace of mind is priceless!
Hope this helps,