First and foremost, you need to understand (or perhaps your CEO as well) that SEO is really a subset of marketing. Seriously, go watch some Whiteboard Fridays and you'll find them talking about marketing in pretty much every one.
Now that we're all on the same page about marketing... what your boss is asking for isn't impossible but very difficult and very much underpaid and overworked. 50 sites and 30 brands... really? For one person? That means each brand is getting, at most, one day of your time. It's a recipe for disaster. But to answer the question...
First, organize the sites and brands. Group them together (spreadsheets can help with this). Try to group by categories and then associate brands with websites. Next, come up with a way to address these. In other words, you can only practically work on one site at any given time. So I would pick 5 sites and set up a Moz campaign for each. Let each run 2 weeks and then Archive them. Moz only allows you 5 active campaigns at a time. I don't know what, if any, limits there are on archived campaigns. Now, assess the 5 reports while you set 5 new ones up and let them run. Rinse and repeat.
Now, for actions, you need to have a list for each website. Again, spreadsheets help here. Document what you do, when you did it and why. Then use Moz to keep tabs on what happens as a result. This will be painfully slow but if they don't want to give you the tools necessary it's the best you can do. If you do get an assistant you can use these reports and lists to delegate things for them to do.
Last but not least, sit down with the CEO and hammer out expectations. What does this CEO want? Does he want you to just make suggestions or is he expecting you to implement them as well? What kind of authority do you have to make these changes? An SEO without authority to make changes is impotent and your job will eventually be called into question (corporations are notorious for mandating things without conveying the associated authority to accomplish them). Try to work with this person to ensure that you know what they want and what you intend to do to get that result.