Simon,
Firstly, my name is Dan Reid, and I work for DocuSign. I am the Product Manager in charge of (among other things) integration, including to Microsoft Dynamics CRM. Let me try to answer your question, and give a little background.
Firstly, DocuSign is an extremely extensible platform. We ship a full set of APIs (REST and SOAP), with full documentation to do almost everything you can do through the UI. (more about that here: www.docusign.com/devcenter).
As a result of those APIs, we partner with hundreds of companies to provide both custom, and "OOTB" integrations. SOme of them we build, but many more are done by our partners.
In the case of Microsoft Dynamics CRM (2011) we built a "Connector" that works with the Opportunity. THe goal of that connector is to make it very easy to install, and get up and using DocuSign. It isn't a complicated connector, and it isn't intended to be. All it does is grab all the Notes and Attachments off the Opportunity, and pop up a "Sending Session" in a new tab to allow you to easily get things signed.
That is a nice thing to do, and works just fine, however, in many cases, our customers/partners want a special flow. They (like it seems you do) want specific (often custom) data to be pulled from an object (maybe it is a simple object like Opportunity, maybe it is something you extended, etc). They want that data to be popped into a document (maybe it is a Word file, or PDF, or whatever), and they might even want that data to "write back" to the source object.
All of that is VERY possible (and actually kinda common) but it is very difficult to put that capability in an "out of the box" product designed to be drop dead simple.
So the short answer is that you can most certainly do what you ask (and you don't need to do mail merge), but you'll need to use the APIs, so you can pass the custom data to the places you need to pass it (and to bring it back).
I don't want to (well... I sorta do, but I'll resist) write a whole novel on which API calls to use, how to do embedded sending, and how to automatically drop data into the correct spots in either a tagged document or a template in DocuSign, but if you'd like more information, let me know.
Lastly, we have many partners (Microsoft VARs) who know DocuSign well, and could help you if you need any help.
Sorry for the long response.
-Dan