If you have your Nintendo 64 roms in the good tools naming scheme then you will need to rename them to the no-intro naming scheme to easily use them with hyperspin. The problem though is that the Nintendo 64 roms from the good tools are in a different format than what no-intro uses(good tools:z64;no-intro:v64) so when you do your scanning with clrmamepro/romcenter you will probably not have any matches or just a few. What you need to do is use tool64 or ucon64 to change the roms to the v64 type. A simple name change will not work as the difference between the two is that v64 is byteswapped and z64 is not.

Extract all your roms and put them into folders in groups of about 200-300 per folder. Doesn't matter what roms go in what folder you just want about 200 - 300 roms per folder. The reason for that is Tool64 can sometimes mess up if you feed it to many files at once. After you have a bunch of folders containing your roms. Download Tool64 from here -> http://www.emutalk.net/showthread.php?t=12075 Open tool 64 and point it at one of your folders. Let it load your roms, select them, and then click edit -> change byte order -> byteswapped. It should go through and byteswap them. Do that for all the folders you made.

When you have byteswapped them all put them back into one folder and run clrmamepro/romcenter and it should now recognize them.

reference: http://forums.no-intro.org/viewtopic.php?f=2&t=409