I have copied over the default theme into my own custom theme and so far it works great. I am having trouble locating what theme file to edit for the helpdesk pages. I want to make some changes to the text found on these pages if possible. ++Edit++ Ok I see where the helpdesk templates are in the main /helpdesk/ directory, but how can I change these in my theme, so that I can still update aMember and not have them get over-written?
You can do it the same way. Create folder helpdesk within your theme folder, and place helpdesk templates to that folder, then edit them.
Yes, just copy files/folder (that you want to customize) from module views folder into your theme folder, and customize them.