There are are a range of third party tools for synchronising files across two or more computers. You mention already using DropBox.
DropBox is designed to sync only one folder. Using symbolic links is a great work around but as you have experienced, the approach is likely to be fragile as it is not the focus of DropBox's developers.
Consider using another synchronising approach that can handle multiple shared folders across your Macs.
Unison File Synchronizer
A stalwart of the file-synchronization world, Unison is designed for keeping two or more computer's files in sync. It deals with edge cases and is aimed at those needing more than just a routine copy between computers.
Unison is a file-synchronization tool for Unix and Windows. It allows
two replicas of a collection of files and directories to be stored on
different hosts (or different disks on the same host), modified
separately, and then brought up to date by propagating the changes in
each replica to the other.
BitTorrent Sync is relatively new and claims to need no cloud and share no private information.
Your information stays yours.
Sync never stores your files on servers, so they stay safe from data
breaches and prying eyes.
Another new comer is AeroFS. For private use a free plan is available. I am not sure how applicable this option will be, but it may offer more options, such as multiple shared folders, than currently offered by DropBox.
Dropbox behind the corporate firewall.
File Sync and Share, for the Enterprise, deployed behind your firewall
rsync is a command line tool included with OS X. You can use
rsync to synchronise file systems with relative ease. Setting up rsync requires a scheduling tool such as launchd, cron, or Power Manager but once done it is extremely reliable.