I really appreciate the response. I read the ePub section that you mentioned. Suprisingly it is the same thing that I keep coming across, so I must be over thinking this whole thing. I attached a copy of a "sanatized" configuration of our switch. Basically what I'm trying to do is this:
PC is connected to back of Shoretel phone. Phone is connected to switch port. We have a DHCP pool specific for phones only, and the way the DHCP server knows to give out the right address, is identified by VLAN. Everything I've read so far, is the way these Shoretel phones work is they boot up on the data VLAN, get their configuration via option 156, reboot and now on the voice VLAN, now when it DHCP's address it gets an IP from the right pool. I explain all that because the port the phone is plugged into is supposed to be a trunk port. Native vlan-id is set so data vlan is untagged. That's why you see it that way in the config.
Interface ge-1/0/27 is the gateway to the Cisco router which is actually behind a fiber switch from our ISP that is in bridge mode (we don't configure it). So how do I allow 802.1q traffic to pass over ge-1/0/27 without losing that IP address? If I change that port to ethernet-switching mode, I can't assign an address to it anymore. In other words, we're using our switch like a router.