Hi @danjenkins:
Apps like Helpdesk, CRM, etc … are independent from ERPNext.
For example, CRM let’s you manage leads, deals, contacts, etc … in a simpler (and well designed) way that ERPNext CRM module does but … it’s not integrated with the whole ERP flow (quotations, customers, etc …), maybe you don’t need that. If you are just looking for CRM … why fighting with the ERPNext “monster”? This is also applicable for Helpdesk.
HRMS is a module for ERPNext (no conflicts)
Books is an simple “alternative” to ERPNext for offline invoicing, accounting, etc … no conflicts.
Wiki is just an tool for documentation, is compatible with ERPNext too.
Check this post (and the whole thread)
Hope this helps and welcome!