Deburr the valve hole by swiping with a small piece of emery paper.
With Presta, use a valve of suitable length. Dont put a long valve into a normal box-section rim, long valves are for deep V section rims. Long valves can be levered about by pumping action.

I use the valve retaining nut to position the valve radially (towards the hub) when fitting the tyres.
I then slack off the nut and push the valve into the tyre so it doesn't obstruct the seating of the tyre bead. Once the tyre is properly seated I tighten it gently.