Not entirely sure what you're trying to do here but probably the best place to start is to review the rights Unity is expecting of the directory and messaging facing accounts. In 3.x we tried to cram all those onto one account but with all the SPs and patches MS has been releasing that set explicit denies on, for instance, the send as/receive as rights on the mailstore for various groups that became increasingly difficult. In 4.x we use two accounts for this and I always reccomend folks do that regardless of which version of Unity they're running.
The Permissions Wizard for 4.0 has a couple help files that run through the specific permission we need for each of these accounts (directory vs. messaging access) and you can get that here:
http://www.ciscounitytools.com/App_Maven4x.htm
I'd reccomend going through that info first and seeing if that answers your question. If not, we can try and get you more details here.
