Originally Posted by J.M.

You can do both and a lot depends on what you mark with and how you mark.

For straight lines I usually 'mark' with masking tape. I do that after sandwiching.

If I mark with a chalk that tends to 'fade' (as in the lines get lighter or smudge or can be rubbed off entirely just by moving the quilt too much) I mark in small sections and thus mark after sandwiching.

Marking with a pen - one that disappears with water - I like to mark before sandwiching because the hard nib isn't nice to use on a soft sandwich.

For a pen that disappears by itself, you either have to mark and quilt the entire thing within several hours (doable if it's a small project) or do it in sections. How long you have depends on several different factors, from the brand to the humidity where you are. If you can do the entire thing in one, I'd mark before sandwiching, otherwise you'd have no choice but to do it after sandwiching. Don't discount the time you need to sandwich it, though, or you'll find your lines have disappeared before you're finished quilting.

If I mark from a printed quilt pattern, I have to mark before sandwiching because I rely on a light box to see my pattern and mark. If I mark with a stencil I can mark before or after sandwiching.

Whatever you do, make sure you test your preferred marking method first ion some leftover fabric to see if you manage to remove the marks. Testing before you mark your quilts saves you lots of tears. (Don't ask me how I know this)