Two more points having read your original post again:

a) in the scenario you outlined, you most likely do not need to "check in" at T3. You should have received your boarding passes for all flights at check in in Brussels (if not, you pick one up somewhere along the way at Heathrow - but you would not have to go landside to "check in", you could do this airside)

b) It doesn't matter how you get from T5 to T3 (just as long as you get to T3 in good time for your flight)