WHMCS is to be installed on a subdomain, will it still work.

So, I am building a new site for a client who wants to integrate WHMCS into their wp site.
I have confirmed with WHMCS support that I CAN install WHMCS on a sub-domain of their main site; my question is, will this be a conflict and will I be able to add sub-domain into the plugin settings?

Secondly, I notice the permalinks are extremely long with the integration of WHMCS into wp, is there a way to 'pretty it up'

That is all for now.
Cheers

Terence