How to restore data from some apps, and not via a full restore from backup?

Based on what I've read, I have some concern restoring my new iPhone 4 from the backup of my jailbroken 3GS (the phone is no longer in my possession). But I have some stuff in my old backup that I'd like to bring onto my new phone without doing a full restore from backup.

What I'd like to do:
1) restore the new phone 'as new' and install all apps 'as new'
2) do a backup of the new phone
3) on my PC, take backup files from a couple of apps and copy them to the new backup created in step 2
4) restore the phone from backup and see data from only the apps from step 3

On my PC, are app backups organized on a 'per app' basis? For example, if i just wanted to restore Awesome Note, is there a file on my PC that I can copy from an old backup and paste into the new backup, with the appropriate data copying over to my phone the next time I restore from a newly-created backup?

Thanks!

 

Oh well; appreciate the clarification. Thanks!