Biomass settling out, dead-zone formation and uncomplete mixing may depend on the propeller geometry and number rather than top-drive or bottom-drive agitation. Schematic presentation would help further recommendation (bottom-drive meaning magnetic drive or motor installed under the reactor). Additionally, full contact of biomass with oxygen should be well established (diffuser type, clogging, biofilm formation, etc) and foaming possibility (if there is any) should affect the reactor design. 

There are 2 basic options for agitation. One is to use a well coupled magnetic agitator from the bottom and the other is a top mounted mechanical agitaor with either a mechanical or liquid seal. If you have  bottom mounted drain valve, then use of a magnetic agitator (large stir bar) becomes more difficult and the top mounted models become more desireable. I have used  both and find that a top mounted agitator to be more reliable. You also have more flexibility in agitator geometry with a top mounted agitator. In some cases, I have modified the magnetic stirrer by adding stronger and larger magnets. This also gives more flexibility in positioning the magnetic stirrer.

Food Biotechnology, Second Edition

Edited by Anthony Pometto, Kalidas Shetty, Gopinadhan Paliyath, Robert E. Levin