Firstly, are you doing any routing on the switches?
I'll assume not... for now so we wont have any IP addresses on the switches for the vlans 2 and 3.
On the 5406 create the new vlans (vlan 1 already there)
vlan 2 name VoIP
vlan 3 name Data
vlan 1 need to have an ip address.
ip address 192.168.1.0/24
now you should tag the uplinks to the fibre connections for both vlans (and leave vlan 1 as untagged).
to do so.
vlan 2 tag b1(or whatever the uplink port is)
vlan 2 tag b2 (etc)
vlan 3 tag b1
vlan 3 tag b2
to make sure they are untagged in vlan 1 you can.
vlan 1 untag b1
vlan 1 untag b2
now on the 3500.
in vlan 1 give it an ip address
vlan 1 ip address 192.168.1.x/24
create vlan 2 and 3
vlan 2 name VoIP
vlan 3 name Data
now on these switches tag the uplinks to look exactly the same as core.
so...
vlan 2 tag 24(or whatever the uplink port is)
vlan 3 tag 24
and thats basically it.
Your vlans are created.
now if you are creating completely seperate voice and data networks there is no tagging of ports required on the switches.
For instance on a 3500 switch you might decide to have ports 1-12 on vlan 2 and ports 13-23 on vlan 3.
to do so.
vlan 2 untag 1-12
vlan 3 untag 13-23
now plug the phones into port 1-12
and the pc's into 13-23
That should be all you need to do based on what you said you want to acheive.