Question about custom tunes on the Gryphon for a 2002 f150

[finalday7]

I'll be ordering a gryphon next week for my 2002 supercrew with the 5.4 and just had a couple of questions. The truck is all stock right now. Over the winter i'll be adding preferbly cat-back exhaust, intake kit, headers and so on. The truck will be hauling a fairly large travel trailer every once in awhile and doing alot of highway driving. My main question is, can I order the gryphon with the stock tunes and say in a few months order up some custom tunes to be installed. Also if I'm using the stock tunes and decide to make modifications will the stock tunes still work?

Sorry for the noob questions but i've always just gone with hypertech programmers so this is my first programmer with "custom" tunning. Thanks