Hi Ben,
With AtoM 2, we began using Twitter Bootstrap (2.3.2 I believe is the most current update we're using), and of course, the layout of everything overall has changed. To my knowledge, there is not an easy way to adapt old custom themes for use in the most recent version of AtoM. I think you would be better off creating a new theme - you can likely copy and adapt CSS elements from the old one, while adjusting them for use in AtoM 2.
The best way to create a new theme is to create it as a new plugin. We include the arArchivesCanadaPlugin as a reference model for developers interested in creating a new theme - it extends the base stylings of the arDominionPlugin theme, and includes a custom home page and custom header, to give a sense to developers of how we have implemented these things. I'd use the Archives Canada theme as your model - you can see what it looks like by navigating to Admin > Themes and selecting it, then saving - the page will reload with the new theme in place.
Once you have your new theme in place, you will often, when setting up the site in development, have to navigate to the new plugin and run "make" the first time, so the LESS compiler applies the theme. It's then advisable to clear the cache, restart your services, and repopulate the search index: