You should go to my site and look for "journey session"
Generally these should be two separate email programs and Smart List A and Smart List B.
Then send a batch campaign to each list.
It sounds like you also want to setup a separate drip as well. There are a lot of ways to do this. I'd recommend, in your situation, just using 1 batch campaign per email per list. Once you have masted that, there are some other methods you could use. Please see docs.marketo.com.
Please provide your site link?