No problem...if it's in a place where you can reach the other side of the panel that has the rust problem, make sure that the rust isn't going all the way through. If it is, you'll definitely want to coat both sides if possible.

I'm using some rust inhibitor on a '67 Bug I'm working on, and found it to be really useful to apply it a couple times...it stops the rust and will leave a solid paintable layer.