I'm not sure I understand what you are trying to do. Are you saying you want additional surfaces on top of the solid?
Then just make a copy of them before the merge. Go into insert mode before the merge and hold down ALT and select a surface, then copy/paste. That will give you an idividual surface. Repeat as needed then cancel insert mode.
If you are referring to a surface on top of a surface that looks bad from the solid and surface occupying the same place, then there are two tricks. One method is to copy the replacement surfaces as noted above. Then color the solid surfaces to be removed any custom color with 100% transparency. Color the remaining surface copies however you like and change the family table accordingly.
A second method is to offset the copied patches by a very small amount so they don't interfere with the solid geometry.
See attached (1st method), is that what you are after?
