no, WiiPair should finish with something like "1 Wiimote paired" and then close itself.
however, the original WiiPair does not seem to work with the TR-wiimotes. but forum-user "uuzi" has made a modified version, that should work with the TR-wiimotes. it can be found here:
http://forums.dolphin-emu.org/Thread-solution-rvl-cnt-01-tr-with-autoconnect
however, the original WiiPair does not seem to work with the TR-wiimotes. but forum-user "uuzi" has made a modified version, that should work with the TR-wiimotes. it can be found here:
http://forums.dolphin-emu.org/Thread-solution-rvl-cnt-01-tr-with-autoconnect