Here is the configuration you should have, if for example you are trunking VLAN 1 and VLAN 2...
3COM:
On the trunk port, set VLAN 1 as an untagged member, and VLAN 2 as a tagged member. Set all of the other ports as untagged members of the desired VLAN on that port.
Cisco:
Set the trunk port as follows:
switchport trunk encapsulation dot1q
switchport mode trunk
switchport trunk native vlan 1
switchport trunk allowed vlan 1,2
switchport nonegotiate
If that works for you, you should have no problems adding in additional vlans as needed.
Please let me know if you run into any problem getting this set up, and I can provide more details, but I'm pretty sure that'll work like a charm.