Create a Project file

Dear all.

Basically i have designed a card. but i have just noticed that the previous guy started design it directly from schematic file and did not create a project.

Now I am wondering if i can create a project and then upload the two file in, if yes how ?. Also The main problem i have is that both design are the equal but the net have different names. Someone know if i will have a problem in generating the Gerber files and so manufacturing the PCB?

Thank you so much for your time 

Cordially 

Antonio