It's so easy to transfer files using the WHM utility for copying an account, it's really ridiculous. I started to do it the manual way - ftp, exporting databases, re-uploading and then I discovered the copy account functions on WHM. So frigging easy and done in a flash. The hard part was getting some of my clients to switch their DNSs to the Harmonmediagroup.com DNS, not the copying of the accounts. Plus, the biggest advantage of a dedicated is a separate hard drive that makes nightly backups of only the files and / or databases that have changed during that day. You can sleep well at night that way, or at least better.
The thing to do is to add up all your hosting you're charging and figure out how much off you would be (or maybe not at all) by getting a dedicated. If it's like $40 you're out of pocket per month, or even $60 after you factor in what you are charging your clients, it is very worth the move IMHO.
So, if I have it right, the transparent software is the add on to the other software you already have installed - sort of like a module somewhat?
As far as learning as you go - sometimes it's the only way. It can be scary, but it will force you to learn what you have to learn to make things work.