Permanently mark pin placement for shirt
Sharpie might work, but will have some bleed on the fabric when applied that may cause the mark to spread farther than would be covered by the pins. Additionally, while you want something "permanent" right now, what happens if you lose the pins but still wish to wear the shirt?

Instead of using a permanent marker, I would recommend getting a hand-sewing needle and a bit of contrasting thread (black and white can generally be picked up quite inexpensively). Thread your needle with a doubled length of thread, then, starting from the inside of the shirt, add a single small stitch where you wish to put the pin. Tie the end off, then add a few more stitches (in either an X or straight line pattern, your choice) and tie off again before trimming the ends. This will give you a visual indicator with no bleeding, that will stay as long as you want it to stay, but can still be removed if the pins are lost or the placement isn't quite right.