Registering for an Apartment (Berlin)

My husband and I are arriving in Berlin on Oct. 1st Protected content begin a process for, hopefully, receiving a Blue Card visa.

My question is regarding registering an apartment, which is required for Visa application. We have secured a temporary flat, through Air BnB, for 3 months but I don't think the owner is going to allow us to register the flat. We can't commit to a longer-term apartment because we only have 3 months before we may have to leave Germany for the required 90 days (if we can't secure a Visa in the 3-month timeframe).

Does anyone have any ideas or experience with how to manage the temporary rental situation with registering an apartment? So much seems to hinge on securing an apartment, but I'm not sure how you are to do this with a 90-day limitation.

Thanks so much,
Lily