What do you plan to use the putty for?  Completely filling the landing gear bay? Or filling the gaps around the bay doors?

Most modelling putties are only meant to fill small gaps and will fall apart if used for larger applications.  The exception are epoxy putties, but these aren't cheap and filling an entire gear bay with it isn't practical.  If you want to completely fill the bays self-hardening clay would probably be your best bet, but this will add a lot of weight to the kit.

In my opinion, the best way would to run scrap stryene across the inside of the bay and then sand to fit the doors and cement the gear bay doors to it. Then you can putty the gaps if needed.