Having a fixed time interval between these checks (so you know when they will happen) instead of checks happening when a counter reaches some number is much better. Configuring this is quite easy. First, look in /etc/fstab . In my case, the relevant lines are:
/dev/sda1 /boot ext2 defaults 0 1
/dev/sda3 / ext3 noatime 0 1
/dev/sda4 /home ext3 noatime 0 1
Now we know which device contains which always-mounted filesystem. To set the checks to be monthly, I run these commands:
tune2fs -c 0 -i 1m /dev/sda1
tune2fs -c 0 -i 1m /dev/sda3
tune2fs -c 0 -i 1m /dev/sda4
-c 0 means no mount counter will be used. If you would want a check at every 100th boot, you would use -c 100.
-i 1m means the filesystem will be checked every 1 month. Other examples of what could be used in combination with -i are 2d (2 days) or 3w (3 weeks).