When installing FreeBSD (sysinstall), just create a separate /squid partition of sufficient size(*), just like you would create a separate /usr, /var, /tmp, etc. FreeBSD will take care of creating the /squid directory in the root and mount the partition on it. Make sure squid owns /squid ([cmd=]chown -R squid:squid /squid[/cmd]) after installing Squid itself.
(*) 'sufficient size' depends on population, but usually anywhere between 10GB and 70GB will give very good results.
Note that it's very much preferable to not only put the Squid cache on a separate partition, but even on a separate hard disk. But even a separate partition is better than using a directory like /usr/local/squid/cache.
Install Squid from ports, and make sure to check the correct transparent mode when you're in 'make config'. (they may all be checked already)
I can't comment on your firewall rules, because I use pf exclusively.
Don't know about your Mikrotic and VLAN setup, sounds contrived to me. Squid usually lives on a router or a bridge with 'regular' networks attached, but VLANs and Mikrotic can work. Not my area.