For the me-109 on the ground would the wing flaps be down or in?

They would be up, but nothing stops you from putting them down on your model!

In many cases the leading edge slats of the 109 would be extended when on the ground. They were extended/retracted by the airflow over the wing, when stationary gravity would cause them to be extended.

After a quick scan through a couple of Squadron/Signal books, the vast majority of the photos show parked 109's with their flaps down. This could be something to do with how long they've been parked up. I know that with the P-51 Mustang the inner gear doors tend to gradualy come down after standing for awhile, as the hydralic pressure falls, though I'm not sure if the 109's flaps were hydralic.

Also, usually you put the flaps down on the ground to stop them from being stepped on by people.

I do that on my aircraft, otherwise they crack since the skin there is under high tension.