If you enjoy the client and the relationship, hang on to it! They are few and far between more often than not.
A few tools we use are: Xero, Toggl, Asana. Always try to optimize your own workflow, but structure it in such a way that it's not all in your head. Your process and hand off is just as valuable as the product itself.
We've had a lot more success tying hours to features instead of defined project scope. Let it creep and change, just be up front with costs and expectations. Realize that your time and work is not flexible, but the feature list is.
Let the client help define the product scope collaboratively with you. You already landed them, so you just need to focus on keeping them.
Since it's not your full time, set mental boundaries for yourself and try to keep the two jobs separate.