On my bike ('91 FXDB-S) the book has you starting in about the middle of the primary cover on the two screws (top and bottom) that are just forward of the swell. Then you move in an alternating top-bottom X pattern forward and backward of that line formed by the first two you did. I like to start with by screwing the screws handy with the bit in a screw driver handle. Then I set the torque wrench at 65 in-lbs. and do the pattern. Then I increase the TW setting to 90 in-lbs. and do it again. Finish up with 110 in-lbs.
Usually it's a cris cross tightening sequence that is covered in the factory manual. Best bet is to get the manual if you are going to work on the bike yourself.