What @Matthew suggested is to configure uplink ports on your various Switches as tagged member for the VLAN IDs you want to transport across them.
As example...suppose you want to transport VLAN 10 and 20 between Switch01 and Switch02 through the uplink SFP port 49 on both switches (or through a group of ports defined on both switches, if you decide to aggregate two or more ports to add resiliency to your uplink) then that port need to be tagged member of those VLAN IDs.
Switch01# config
Switch01(config)# vlan 10
Switch01(vlan-10)# tagged ethernet 49
Switch01(vlan-10)# exit
Switch01(config)# vlan 20
Switch01(vlan-20)# tagged ethernet 49
Switch01(vlan-20)# exit
Switch01(config)# exit
Switch01#
So that port 49 will be untagged on VLAN 1 (Default) and tagged on VLAN 10 and 20. Repeat the same for Switch02.
The same if you have a LACP port aggregation: suppose you aggregated 49+50 on Trk1 with LACP (trunk ethernet 49,50 trk1 lacp): instead of referencing to physical port 49 you must reference to trk1 (which is a logical port).