It needs to be low viscosity (runny) so that the air bubbles all escape.
Many potting compound vendors point out that you can evacuate air bubbles by putting the freshly potted module into a vacuum chamber with a slight vacuum. Obviously this requires some extra equipment but it might be an option for what you're doing.
I can also tell you from personal experience that epoxies are far easier to keep bubble free than urethanes, which are also often used for potting. The latter are often preferred due to their softer cure (less risk of fracturing SMD's, particularly MLCC's) but our experience has taught us that epoxies yield better overall results in production. You can get epoxies with lower durometers if you look around, which helps offset the risk, and using a slower cure compound helps too. The one we use has a pot life of around 30 minutes and a full cure time of 24-48 hours at STP.