I found out how a while ago, I just forgot to update it here:
RunWait("REG" & " LOAD " & "HKU\Pos C:\Users\Pos\NTUSER.DAT", "", @SW_HIDE)
RegWrite("HKEY_USERS\Pos\somewhere", "1", "REG_SZ", $value)
RunWait("REG" & " UNLOAD " & "HKU\Pos", "", @SW_HIDE)
This is basically how it's done. Just load any user hive by using RunWait(). Then do anything to it like it's a normal registry. Then unload the hive.