We need to know a bit more on the context, a network diagram perhaps ?
Simple drawing on paper can be enough.
General advice:
1 bridge on your router, unless you have a real good reason to have multiple which for most, myself included, means if you do not exactly know why you want to split, keep it with one bridge.
If your different subnets all terminate on a different ether port, you can do without vlans.
But you mention Fortigate. Only 1 or 3 different ?
Otherwise (and for future expansion) vlans are the recommended approach in most cases.
Some “light” reading on the matter (ahum …) and THE reference around here:
http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1
(read it, digest it, read it again, experiment, …)
But we really need to see more context in order to give you better answers.