Confused about whmcs Integration with WP or Joomla

[Jowwow]

Hey guys, perhaps you can help clear this up for me.

First let me state I'm a rank noob

I'm seriously considering replacing my current template and config with "a more modern, responsive, flat style" that my friend is recommending I convert everything to. No specific template just seems to be less bling.

My problem is afaik if I integrate WHMCS into Joomla ( seems to be difficult to do ) then I've got this folder called "whmcs" sitting out there easily bypassing my install.

same with WP.

Another is I use Joomla to handle my software distribution and probably more then anything else cause I've used it for the last 7+ years and just really comfortable with it.

I don't think whmcs can do software distribution as well as Joomla can and I know zero about wordpress.

 

So any and all feedback, recommendations, edification will be greatly appreciated.