I loved trying to mix different media and came to a lot of neat combinations. For example I realized that sharpie and acrylic are great together. Even years later my paintings still look fine with no purple fading in the blacks.
Now I actually use the more art friendly versions of artist sharpies which produce a nice deep black, but if the regular ones work for you use them. The sharpie oil based paint pens are better than just the traditional old sharpies but not perfect. Just a darker black.
Now when I use them I outline first with sharpie then go over in paint pen. And I have never had color or smearing issues while sealing them.
I would also suggest giving the sharpie a day or so to dry before glossing.