This is really a matter of personal preference.
As a guide, you could space your nails so there is one nail every couple of boards on each panel. This would be more than enough so if you choose to space them further than this, it's not a problem. When securing the sides to the floorpanel, you should nail through the framing into the floor where the bearers are. The position of the bearers will be easily identifiable by the run of nails through the floorboards.
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