I'm installing a new Nagios 3x and NagiosQL3 server running SLES 11, importing parts of an old Nagios 2x/NagiosQL2.

I had misccommands.cfg and checkcommands.cfg separate in my old config, and would like that still. It appears that nagiosql3 has put both misc and check commands into one file, commands.cfg. Is there a way to split these?

Alternatively, could I use cfg_dir in nagios.cfg and have each command in its own file?

Nagios itselves uses only one command file since long time. With version 3 NagiosQL uses also only one command file.

There is no option to split these commands. You can import them using two files - but writing is only possible to one file.