Yes, you can definately do that. The only down side you might run into is that it will take quite a bit longer to cycle your tank. There are two basic approaches.
Rubber maid tub, heater and a power head. This allows you to cycle the rock but be able to drain the water off the rock and replace it relatively easy. This will remove more of the detritus from the rock and water which, in turn, makes it cycle faster.
Rock in tank....
This approach produces a much stronger tank after the cycle, but can take quite a bit longer to cycle. There is more detritus in the water for longer periods of time. That means the toxic leves stay up longer which causes more die off....which prolongs the cycle.
It has been my experience that more of the life on the rock will survive with the first approach due to the lower levels and shorter exposure to toxins.