If you have mapped singular faces and assigned different materials or textures then yes they will disappear depending on which is selected in the UV edoitor viewport. ( If I have this right?). Can you please post a screen shot on what you are doing Brady? this will make it a lot easier to solve. I am assuming you are trying to UV and texture a singular object? not multiple? If its a singular object (geo shape depending) in Create UV there are quite a few options on how you want to UV......
"A Darkness at Sethanon", a book I aspire to model some of the charcters and scenes