My pump house is set up for a shallow well I need deep well application and just have a question can I go straight from the pump and then go 90° up over and then down or will I get air in the lines

You will not get air in the lines.

Are you talking about putting in a submersible pump, or a deep well jet pump?

Either way, you are not going to get air in the lines UNLESS the pump is drawing in air due to a lowered water table.