I just had my FUT surgery two weeks ago. How long should I wait to cover my surgery line with SMP at back?

You need to discuss your case with a doctor.  In general you need to wait until your scar has healed and the doctor feels comfortable with starting the SMP process. 

Scar tissue reacts differently to the scalp pigmentation compared to virgin skin. It takes time for a strip scar to relax and settle down. Most strip doctors will not want to touch an existing strip scar if it less than 12 months old and fully relaxed externally and internally. Pigment can take longer to take on scar tissue and fade faster on occasions. It may take more sessions to complete a full result to blend with the surrounding hair and remain stable. 

Hello!  Ideally it is best to wait until the the donor area has fully healed.  It can sometimes take months for that to happen.  We generally advise waiting 6-12 months, depending on how you healed.
Good Luck!

I generally like to wait until the surgical scar is completely healed, usually a few months at a minimum to get there