So far I think I need to bin off my existing bridges, combine everything apart from WAN into one bridge, and then VLAN?
Indeed. I like to think of VLAN as layer 2.5 ... so physical connections (ethernet, layer 2) get overlaid with L2.5 network which logically speaking has different layout than L2 network. VLANs, being virtual, are harder to visualize (that's easy with L2 being physical), so perhaps some drawings on flip chart or some such may help.
Could be the best approach is top-down: make list of your devices, divide them to different IP subnets (that's L3). Then you make out connections needed and that will be your L2.5 network. When L2.5 network is known, design physical connections (L2). If it turns out L2.5 and L2 networks are 1:1, then there's no need to add VLANs into mix, perhaps split horizon is all you need (to segment a switch). Or another (thought) approach: after L3 design is done, only consider L2 (physical connections). If there are many physical connections (used by different L3 networks) going from geographical point A to geographical point B (both points can be either end-device such as multi-homed server or a network appliance such as switch or WiFI AP or simply cable aggregation point) but you can't really implement them in physical world (read: no more space in that duct pipe), then you add the L2.5 on that stretch.
And if you find out that there is need for VLANs anywhere in your physical (l2) network, then implement VLANs on all LAN devices end-to-end.
Then it comes to configuration of MT bridges. Yes, if they are supposed to participate in VLANed network, then the proper way is to configure them as VLAN-aware switches which means single bridge with
vlan-filtering=yes. Remember: nowdays basic functionality of bridge is spanning
physical interfaces, VLAN is a function of bridge (not the other way around).
And, to make your head spin even more but perhaps you'll find it useful: it is possible to use VLANs internally to single switch/bridge. This way it's quite simple to segment a switch and keep HW offload on all ports at the same time (by configuring two bridges one looses HW offload on one of bridges).
BTW, sometimes it's useful to treat WAN as one of VLANs as well. E.g. if you want to create router-on-a-stick where WAN is connected to one of switch ports, another switch port is used to connect router (and router only uses single physical connection for all involved networks, WAN being merely one of those networks). Philosophically: what's the difference between WAN and any of multiple LANs? Apart from more strict blocking of ingress connections in firewall and default route pointing at some WAN-connected router not much. Doesn't really differ in terms of L2 or L2.5. And yes, it is completely fine to run tunneling protocols over VLAN (e.g. PPPoE).