Can I separate rental properties in 1 QF Company?

I would advice either set up a new nominal code for each property, or what may be better is set up a project tag for each. With a project tag, you would be able to analyse profit/loss, income and expenditure for each too.

Take a look here for tag info:
http://community.quickfile.co.uk/t/projects-in-quick-file/1591?u=parker1090