The simple answer to your question is yes you can. But why bypass the system?
Why not consider just pulling the fuses and circuit breakers to everything but the air conditioning feed. That way you can inspect and/or trouble shoot without fear of electrocution and once you are sure the circuit you are working on is working properly, you can reconnect it to the system.
You would also need to disconnect the cables to the negative terminals of the chassis and house batteries.
Of course not knowing anything about your system, it is hard to determine how many CBs there are and how many house fuse panels there are, therefore, finite instructions are impossible to offer. Just remember, it isn't rocket science, it just looks that way at first.