I am a longarm quilter but I did a lot of FMQ before getting my longarm.
If I have a specific design on the quilt, I usually mark the whole quilt first. Another thing is to use a very thin paper, I prefer tracing paper, draw the design, and stitch the drawing. After removing the paper, you may still have tiny bits caught up in the stitching but washing in the machine will remove those.
Hope this helps!