NOTE: Use your Service Manual for torque specs or Click Here for OEM torque specs in the Sportsterpedia).

The factory service manuals lay out the procedure for 'stripping the motorcycle for engine repair'.
This covers the procedure for removing / installing the motor and also includes the motor mounts. However, the whole story is not in the manual.
You can induce added vibration and potential for cracks in the mounts or cases if the mounts aren't installed properly.
Below is the procedure from the manuals for removing and installing the mounts.

To remove the motor mounts (given all other particulars have been removed as this is strictly regarding the mounts themselves);
Note: Drain engine and primary oils before removing the engine from the frame.
The order of installation should be done as numbered below.

1. Remove top center mount:
   Remove the both bolts to the frame, nutplate and shim(s).
   Remove both bolts and washers from the heads and including ground wire for VOES (if applicable).
2. Remove upper front mount:
   Remove both bolts and washers from the frame along with nutplate.
   Remove both right bolt and left nut and washers along with the mount bracket.
3. Remove lower front mounts:
   The upper rear bolt is threaded into a welded not on the right mount plate.
   Remove the bolts and their respective nuts and washers along with the mount plates.
4. Remove rear mount bolts, nuts and washers from the frame.
   

To install the motor mounts (Again, this is strictly regarding the mounts themselves and all other parts will need to be addressed that were removed).
The manuals simply states to install the bolts loosely in each mount along with the respective nuts and washers.
Then tighten the bolts per the FSM specs. See the link to OEM torque specs in the at the top of this section.
The order of installation should be done as numbered below.

1. Install rear mount bolts.
2. Install the lower front mounts.
3. Install the upper front mount
4. Install the top center mount.