You can’t use 2 different logos. However, you could use the same logo and a note in the footer or something?
Reference:
http://community.quickfile.co.uk/t/are-you-able-to-run-2-divisions-under-the-same-accounts/4716/4?u=parker1090
http://community.quickfile.co.uk/t/setting-up-quick-file-with-a-few-different-trading-entities/2577/2?u=parker1090
@Glenn’s post here may be of some help too:
http://community.quickfile.co.uk/t/consolidated-entity-accounting/1611/5?u=parker1090