logrotating files in a directories and its subdirectories

How deep do your subdirectories go?

/var/log/basedir/*.log /var/log/basedir/*/*.log {
    daily
    rotate 5
}

Will rotate all .log files in basedir/ as well as all .log files in any direct child of basedir. If you also need to go 1 level deeper just add another /var/log/basedir/*/*/*.log until you have each level covered.

This can be tested by using a separate logrotate config file which contains a constraint that will not be met (a high minsize) and then running log rotate yourself in verbose mode

logrotate -d testconfig.conf

the -d flag will list each log file it is considering to rotate.