Hi,
As Mum24kids mentioned, you can use the two together. You can find out exactly how to link Manager and PEX in the 2009 Summer Enhancement Guide located here
http://www.ptotoday.com/manager/manual.html.
When you decide to use PEX for your email client, you can still use the VB email system. All general emails are sent out through PEX (emails that are generated by going to VOLUNTEER BUILDER _ FIND VOLUNTEERS or SETUP _FIND USERS. If you have an event specific email, the email can be sent through the event section using VB. The same is true if your run a report such as the student report and then select "email this list". The email will be sent via VB and not PEX.
Hope this helps - feel free to call us at 800-557-2670 if you need additional help.
- Mike