There are various ways to tag and untag packets with their VLAN numbers, and various ways to associate packets with different VLANs. People use them to join disjoint networks as one logical network, or to split up high priority traffic from other traffic, amongst many other uses.
I prefer to keep them simple, and stick to port-based tagging - I find it easy to visualise, and thus easy to work with. I use the managed switch and VLANs to give the Linux server/router multiple virtual ethernet ports.
The trick is to make each port on the managed switch into either an untagged port on a single VLAN, or a tagged port on multiple VLANs for trunking. Trunk ports are only ever connected to trunk ports on other switches, or a port on a Linux box configured with virtual ethernet ports to match the VLANs. This way traffic on a port is either untagged and on a specific VLAN, or tagged and carrying multiple VLANs, which can be split up later by another switch or by a Linux box.