I usually connect fans to the headers then use Speedfan
to monitor the temps. Speedfan can utilise RPM monitoring but doesn`t necessarily have to use it. With a two pin connection to the fan headers it will monitor the temperature and adjust the speed, the only thing it will not do is report back on the RPM speed. Many fans do not have RPM sensors, but these can still be connected to the fan headers and controlled via speedfan direct from Windows.
The only outstanding issue in this subject is one that has not been mentioned, but very important. Before connecting any fan to the fan headers on the mobo it is of paramount importance to check that the power requirements will not exceed that of the header. Thus, check the fan/packaging/paperwork against that of the mobo/shuttle manual and make sure the requirments do not exceed the fan headers. Failure to do so may render the fan header(s) completely unusable, as in blowing them completely. This has happened to many users, so be warned when messing with electrickery