I use pen both before and after, depending on what I’m painting, but mostly before because I like to use it to establish my values.
There are a lot of variables that affect your pen when using watercolor – how much pressure you apply, the tooth of the paper, the paint itself. Paints that granulate have particles that can clog a pen and even worse, if they have mica to make them shiny, they can be death to fabric tip.
I’ve found Microns to be the most delicate. Pitt artists pens and Staedler are better. I’ve had the most luck with my Zebra Zensations Technical pens. But none will survive if you are applying too much pressure.