Kari,
You are trying to make a very simple procedure into one very complicated!! It is my understanding that you are questioning the use of mats as spacers under the top mat with multi-openings and different colored mats under for each opening, correct??
If so you don't have to worry about stacking all these mats on top of each other and cutting out only the openings that will show in each window. When I use mats or foamcore for spacers I always use strips unless it is convenient to cut the openings which isn't often. You can cut your different colored openings in small undermats, secure them around each appropriate opening, and then fill in fairly close with strips of matboard to build up those areas that need building. You don't need to attach each piece of filler mat directly to the other or to the opening mats. If it makes you feel better you can use linen tape to secure each to the other but that isn't the least bit necessary to do. I usually don't cut the spacer pieces close enough to get them tight against the adjacent mat piece.
So you can have 5 or more openings with a different colored reveal in each opening and you can fill the voids with matboard strips without too much precision and all will be right with the world.
Framerguy
Edit: Regarding the adhesive I guess you can glue them as Cliff suggests but I have used ATG for attaching mats together for the past 18 years and have had a total of zero people come back at any time with any complaints of my mats coming apart or "migrating". When you sandwich your mats between a sheet of glass and a piece of whatever backing board you prefer there is little chance of them moving anywhere under normal handling conditions, ie., delivery to customer's home, installation on the wall, and static display for many years.
If your customer is going to throw the art package at his/her spouse during an argument I would suggest gluing with Maxim or CornerWeld.
Edit to 1st Edit:
Maybe this is an exception for using glue on the mats. With small strips of mat filler, you may be better off gluing them down rather than depending on ATG alone simply because it sounds better and will appease some of the "gluedown" diehards.