Your explantion of the problem is ambiguous.
On each disk there is a hidden PoolPart folder. In Windows explorer you must enable view > hidden folders to see it.
Everything in these folders is part of your Pool. Anything on the disks but outside these folders is ‘Other’.
If you want to force files into the Pool - for example using another system which does not have Drivepool installed - you have to move them into the hidden poolpart folder. This practice is discouraged because it can confuse Drivepool or cause errors. But if you must do it follow the instructions on Drivepool website/forum.
If you just want a compressed system image, Windows has this functionality built in. Control Panel > Backup & Restore (Windows 7). It’s basic but free. It doesn’t support versions or multiple images so you have to change folder names if you want to keep more than one image.