EDIT: I just realized you weren't talking about JUST remote service checks so, unfortunately, I need to change my answer to "you can't". If you want to change the timeout settings for service checks then you must apply it to all service checks in the main configuration files.
You'll need to define a second command argument, one that uses your special timeout setting.
For example, this may be your original check in commands.cfg:
define command{
command_name check_nrpe
command_line $USER1$/check_nrpe -H $HOSTADDRESS$ -c $ARG1$
}
And this would be your identical command with a longer timeout value (also in commands.cfg):
define command{
command_name check_nrpe_slow
command_line $USER1$/check_nrpe -H $HOSTADDRESS$ -t 120 -c $ARG1$
}
If there is a better way to do this nagios-wizards please let me know! It would save a lot of room in my own configuration files.