We are currently looking at Sunday to Wednesday, arrive midday to
Brussels from London on eurostar on the Sunday and depart at around
5pm back to London via eurostar on Wednesday.
That's really only 3 nights/2.5 (maybe) sightseeing days so I'd spend the entire thing in Bruges. Go directly there after arriving in Brussels, and return to Brussels after check-out on Sunday. If nervous about making it back to Brussels for your Wed. flight, then you could do Sunday-Monday nights in Bruges, leave later on Tuesday, and spend the pre-flight night in Brussels. You did't mention what time of year you're thinking of taking this trip?
You also haven't given us any idea what you are interested in doing/seeing while in Belgium but there's plenty to keep you occupied in Bruges IF you are interested in what she has to offer. We spent 4 nights/3.5 days there (minus a day trip to Ghent) and didn't cover it all.
We did spend 1 night in Brussels, and it didn't appeal to us as much as either Bruges or Ghent.
Editing to add: good reminder above about museum closures on Monday throughout Belgium; another good reason to spend both full days in Bruges. Some of the attractions which ARE open Mondays (or were recently) are Beguinage Ten Wijngaarde, virtually ALL of the historic churches (those alone could keep you busy all day), City Hall, the Belfry, the canal boat tours, and, of course, walks around the squares and many architectural points of interest. Do the museums on Tuesday.