Luckily, 301 redirecting from one site to another (when moving a site) and using the Google Change of Address Tool has taken out a lof of the risk that used to exist. if done properly, you should benefit from combining both sites and not lose any rankings.
You're on the right track, I would outline the content and make sure that there's not any content that overlaps--every product/service and every page should be unique and not cause any duplicate content issues.
Generally speaking, you'd want to do what you're planning, which is to use a directory off of your main domain and then 301 redirect the pages from the old site to the new pages on the new site. Use the Google Change of Address Tool to tell Google about the change.
I would fully integrate the pages into your main navigation on the site rather than just provide a link--it's important that the new pages get all the internal links that they can.