Right now, the Account Owner in MS CRM is the integration user.  There NEEDS to be a way to Map the Quickbooks Sales "Rep" to the MS CRM Account "Owner".  You should also have the ability to MAP either one to one or many to one.

e.g. 

QB "REP" = MS CRM "OWNER"

QB "JDOE" = MS CRM Account owner "John Joe"

and/or if the MS CRM Owner is responsible for other sales rep's Accounts, you should be able to map multiple QB Reps, to a single Account owner in MS CRM.

If this is done correctly, the MS CRM user should be able to look under accounts, and see only their appropriate accounts, orders, invoices,quotes, contacts.

In addition to the above, the QB "REP" should be displayed under a custom field in MS CRM.  This way, the MS CRM user knows who the last sales rep for an account was.