In the middle of the registration process of WHM Autopilot and 2checkckout.com I found out that there was some issues with domain registration with WHMA + 2co.
I've searched the forum and found out the only option is enom.
I'm currently with registerfly.com and I'm satisfied with the $9.99 domains (let me know if you have a better site) they have. I don't want to buy i.e .com domains for $29.95 from enom no matter how automated the process is; It would be like throwing my money out the window. But (correct me if I'm wrong) if I use i.e mypaysystems and WHMA, will I than be able to autoregister my domains at registerfly?
I'm not sure about using registerfly with WHMAP, but I can tell you that getting a reseller account with eNom is a lot cheaper for .com domains than 29.95.
Go to eNom's site and sign up for a reseller account, they will email you more information about current reseller pricing, etc. You will not need to complete the process if you decide against it. You can also look for another eNom reseller who may be offering cheaper plans than eNom itself because of the larger volume.
I decided to go through eNom directly because if you purchase service from a reseller, they are the ones who will be providing your support. I'd rather get support from the main company itself.