Is there any way on the LOT App/website that I can have them remember and use my LH M&M number every time I check in without having to manually re enter it.

I add it when I make the booking. Its there, the booking automatically appears on my LH app. When I come to check in for the outbound the LO app tells me there is no frequent flyer number, so I add it manually. Then when I check in for the return again I am told no frequent flyer number and manually add it again.