You will add vlans the same way as you would with other interfaces.
Post your attempt with vlan config here and we can see where you going wrong and can try and assist you
Connection should be as the following, Server > Mikrotik CCR1036 > VPLS > Mikrotik CCR2004 > Server.
I am trying to make both server communicate through VLAN "2". I have added the VLAN and allowed it through the port towards the server and through VPLS link.
I have bridged both VPLS and Server's port as well.
Flags: X - disabled, R - running
# NAME MTU ARP VLAN-ID INTERFACE
1 R Server-2 1500 enabled 2 ether4
2 VPLS 1500 enabled 2 vpls21
3 Bridge-VLAN 1500 enabled 2 MGMT