For pool miner: use -d (start with Nth device instead of 0) and -t (use N devices) command line parameters.
Examples:
-d 1 -t 1 (use second GPU only)
-t 2 (use 2 GPUs only)

For solo miner:
"device_index" option in miner_conf.json file (it's like -d option above)
--mining-threads command line parameter (like -t above)