WHM and WHMAP complement each other - one doesn't replace the other.
WHM (and cpanel) is used for actually hosting the sites and working with the server.
WHMAP is used for billing, client area, order form etc...
You would use WHMAP to bill users for accounts, and WHMAP will then create the hosting account in WHM. WHMAP doesn't replace WHM, it complements it.
There is a utility within WHMAP to get a list of your accounts in WHM into WHMAP. As disoft said, it'd probably help if you searched through the whmap forums as you'd hopefully understand a lot quicker what it does and how to do it
I'm not totally lost. I understand that whm manages the accounts, and that whmap manages the billing/tickets, but a lot of controls overlap, yet seem not to work with how I have things set up.
I've been looking around a lot, and I can't seem to find much more than bits and pieces of information...
For example, I tried automatically setting up an account through whmap, to also create an account on the server at the same time. I filled in the correct information, pressed go... and nothing happened as far as the server goes. So, in an unrelated search, I found that it's A) Not possible without root or B) Only possible when the account packages are identical in both whm and whmap or C) a combination thereof.
You might want to consider posting on the WHMAP forums or submitting a support ticket. You'll get better support that way
Anyway, what you need to do:
1. Setup server with WHM access key - you don't need to be root, just a reseller.
2. Create packages in WHM. Then create the same packages in WHMAP (if you had root access you wouldn't need to do this). Packages should be in the form resellerusername_packagename, not just 'packagename' when setup in WHMAP.
3. Away you go
If that isn't working, I really do suggest reading the WHMAP forums ( there are plenty of threads that cover this), and then post in the forums or submit a support ticket if you can't get it to work.