If your switch ports are all in the same VLAN, e.g. if one of the switched is an unmanaged switch, then you don't need to use a trunk port. If you're not using VLANs, just link the switches using a standard port.
If you use .1q as your trunking protocol, it leaves frames from your native VLAN untagged (VLAN 1 on Cisco switches). Traffic from this VLAN *may* pass through a non-trunk port on the other switch, but traffic from all other VLANs won't.
i.e. unless both switches are capable of trunking, using the same trunking protocol, etc, don't use trunk ports.