I am trying to develop everything in sharepoint as features so I can easily deploy to test and live sites without having to do any manual steps.
I can deploy my master page okay, and though currently i have to switch it on by hand I am confident I can automate that in the future.
What I am having difficulty is getting a CSS file to match up with it. I have created the file, and I think i am doing the right thing so it is deployed in the sharepoint install, but I cannot work out how to link it to my Master Page.
There must be a right way of doing this but I cannot find it!
I believe you are looking for the <SharePoint:CssLink> tag. The link below has quite a bit of detail about it (among other things):
http://www.cleverworkarounds.com/2007/10/08/sharepoint-branding-how-css-works-with-master-pages-part-1/
This site is also a good one to take a look at, since Heather Solomon is the SharePoint Branding Queen: http://www.heathersolomon.com/blog/archive/2006/10/27/sp07cssoptions.aspx