Got the engine mounted inverted, and it will be cowled. Carb and fuel tank line up pretty well, so flooding shouldn't be an issue, so where should I put the fuel filler valve??
Can it go above, or below the plane(as in line[not fuel line]) between the tank and carb? How far is too far?

If you haven't already bought the filler valve, I assume you mean something like the dubro quick fill valve, consider a fuel dot with a 3 line tank instead. Mount it high enough and with enough slack that you can have the end near the top of the tank. If you are going with the fuel valve I try to put it somewhere between the tank and carb to minimize the amount of fuel line.

Placing it slightly above or below the normal fuel line run should have no effect. As Chuck said though, try to keep line length to a minimum without kinking.