These different options you are referring to are templates which can be used as starting point to build a FLUKA input file. In Flair you can then add extra physics cards or further edit the geometry to your liking. The ‘lattice’ option refers to the functionality in FLUKA that can copy a subcomponent of the geometry several times, hence it does not refer to the lattice defects you want to study. I believe for your purposes the ‘basic’ template should suffice, in here you can include the RPP body representing your diamond detector and also include the proper physics and beam cards.
To quantify lattice defect related quantities such as dpa I can refer you to some previous discussions on the forum on dpa calculation and residual gas production. Hope this is helpful!
Cheers,
Andreas