There are two mikrotik, WireGuard channel between them, on top of this channel I raise EoIP, but the traffic still goes through WG.
WG and EoIP configured as described on the site help.mikrotik.com
Question: how to direct traffic through EoIP?
Remove routing via Wireguard ?
Think of it this way, you have to establish the connection between MT devices through wireguard and then tunnel through wireguard to do the EOIP work.
The firewall rules required will allow EOIP traffic to subnets/internet etc…
Not familiar with EOIP but for L2TP this was the basic premise.
(1) Create WG tunnel normally, just basic connection/parameters aka the handshake.
(2) Create the handshake for EOIP through the wg tunnel.
(3) Through FW rules allow EOIP traffic on both devices ( external to local and local to external)
(4) Ensure routes for above traffic are created for local and external traffic through EOIP gateways.
thx a lot 
@Frankxo, could you please share an example of the usecase for EoIP with Wireguard and, if possible, the CLI part of how you implemented it?
Thanks