Glad to hear that it worked well for you.
Winbox is great for seeing a lot of information really quickly, but a lot of the power of the MikroTik lies in the CLI. It's much easier to make massive configuration changes and updates via the CLI than it is to edit one thing at a time from the Winbox.
Routing is relatively straight forward, but can be very complex. The 0.0.0.0/0 in dst-address is a catch all, that is supposed to represent all IP addresses, so the router knows that all traffic that doesn't match a more specific route, send to this IP, and that router will take it from there.
There is no real central storage that I am aware of provided by Mikrotik. Also the .backup files are meant to only be used on the board that they came from, and if you try and import them on a different board, it will usually come out with a semi-broken config. The best option for getting a config from one board to another is by using the export command, this writes out all of the commands it would take to get a MikroTik to the state that that one currently is in.
Here's the link to the Wiki page with multiple VPN examples:
http://wiki.mikrotik.com/wiki/Tunnels
One thing to keep in mind, a LinkSys hides almost everything it has set up and the options from the user and are not accessible at all, but since it assumes a lot of these things and has it set up for you, it is a lot easier to use, but not nearly as powerful. Where as the MikroTik gives the user all of the options and is extremely powerful because of this, but you are expected to set up all of the options that you want yourself and assumes very little, so has it can have a very steep learning curve. The main thing to remember is not to become overwhelmed with all of the options and focus in on the one thing you want to accomplish and work out from there.