When I started out, it was a slow learning curve figuring out exactly how SFDC and Marketo were synced and talking to each other - I wish I had taken more time to understand this, and understand the database better in general, particularly custom objects. It would have saved me so much time.
Also - programs and program statuses. In my early days of using Marketo these didn't exist so I can't exactly say I would nail these better if I started again... however if I was giving my top tip these days to new users - understand your program statuses, get them right, build custom channels if need be, and put in the discipline to use them on EVERY program. Once you start digging into reporting and you haven't done this, you start to realise how vital it was to do.