The real answer is you need inner tubes with longer valve stems. Tubes come with various length stems to accommodate deep section rims.
There are screw-on valve stem extenders available for both Presta and Schrader that you could use to extend your stems. (I think some Schrader ones are actually for car tires, but they would still work for a bike.)
With out an valve extension, to get started, try pressing down hard on the tire and tube opposite the valve stem to press the it out of the rim so you can get the pump nozzle attached. Having someone to help you will make this easier.