Mikey, when I ran singles and used queen excluders, it was tough to get them to draw comb on foundation above the excluder unless the flow was pretty intense. Even then, I bottom supered so there was at least 1 box of honey above the foundation box. When the nectar is gushing, they would draw out unwaxed foundation above the excluder without any problem. I went fishing for 2 weeks about 10 years ago and had a yard that had lots of potential but I was out of comb. I put 2 deeps with just foundation and I had 2 big boxes of honey when I got home--I was lucky!! My best luck at drawing comb in supers was to place the foundation frames at the #3 and #7 position in a 10 frame box that had 9 frames. That has been true for me (and others here in North Dakota) for singles with excluders or doubles without an excluder. Most commercial folks do not use an excluder on doubles, especially those that only pull honey once a season. They do get up and lay a little brood in the 3rd box but they have generally hatched and the cells are backfilled with honey by harvest time. Every area is different but I'd think I'd toss the excluder for now and just put your foundation box on top and see what they do. The worse that could happen is that you might get some brood in some of the frames but, if it works, you'll get some comb. Once they draw out most of the comb, shake your bees back to the 2 lower boxes and put your excluder back on if you want. Any brood will hatch and since the excluder is there, the queen won't lay any eggs and they will get back filled with honey when you have your next flow. Once you get comb drawn, you can mix it up with foundation (like the #3 and #7 frames or some other combination) and get comb for honey production. Having drawn comb next to your foundation frames will help and serves to bait them to the box to make honey, whether you use an excluder or not. Having an excluder separate a new foundation box and the rest of the hive is doable but the bees will need a real strong flow in my opinion.