Do you use gesso when you paint? If you don’t then i’de try applying a good amount of gesso before laying down your pen work. That could help with the bleeding.
I personally never use pen because I find it just shows through any sort of painting which I’m not a big fan and it’s also harder to fix any mistakes once drawn. If you want to be able to see your lines better without using a pen then I would use a thicker/darker pencil. You just have to be really careful with it because although it usually doesn’t smudge with paint or water it can smudge very easily with your palm. Using a darker coloured pencil will also make it show through the painting, if that’s your desired look. However I would also be careful about what brand you use. Try getting a brand with a harder graphite so it doesn’t muddy the water or painting, also try using less water if your going to do this method.
Ok so I'm a new kind of stupid... I like to ink my drawings before I add watercolor and I don't have like a trusty pen, some are waterproof others aren't I usually just test random ones to see if they are waterproof. Any wayyy, my dumb self just inked an entire drawing in non waterproof pen. I would really like to add water color cause this one of the few drawings that I actually like alot lol, so does anyone have ideas for what I can do so pen doesn't smudge every where or is this a lost cause?