I made the big mistake of initially gluing the port-side wedding cake sections onto the base plastic and then attempting to drill holes through both. DON'T DO THAT if you are using bits smaller than .50 unless you are a consummate drill master. I am now drilling after I greeblie each section due to the thicker plastic of the base that has already cost me about 26 .030MM micro bits for the eventual .025 FO I will insert for lighting. I did not have the problem with broken bits with the trenches due the fact that I carved away the base plastic because I raised the trenches by .060 MM. The thinner plastic on the greeblied sections is not a problem, but when trying to drill through those AND the base plastic - *snap*! Goodbye bit. Each and every time I tried.
I found it is easier to drill the greeblied section faces separately, then holding them on the base section they will be glued to and marking where the holes are through them into the thicker base plastic. I can then drill those holes with a much thicker bit very easy, clean it up and then glue the greeblied plate over that section. Will make it easier also I think to feed the FO through. Wish I did that for the front lower cake section.
Tried that on the front two forward facing sections of the cake when I started on the wedding cake after the trenches, bays and engine areas were done. Drilled a hole, then tried to score the plastic with my trusty #11 so I could bend and snap out the 'window'. Ended up cutting my thumb literally to the bone and bleeding all over the top of the model. Blood, sweat and yes tears being put into this baby. So given that experience and my fears of the integrity of the framework holding up and not warping over time - I decided to try my luck at just drilling through both the plate and the base, and when that cost me dozens of microbits - I went with the method I am using now.
More alterations...removed the greater part of the internal dividers behind the trench pieces (bring down structure appeared) with the goal that fiber optics won't get guillotined lol. I cleared out the regions where the parts enter into the dividers with finding pegs; there is a lot of sticking surface over the trench parts for the upper structure.