I'm working on setting up a small business with IP Phones to connect to the Asterisk Server. Now, for simplicity we just ran 2 CAT5e lines to each room, and 1 was hooked to a phone jack, before my VOIP plan was approved. The VOIP phones we got have a port to connect to the computer as a switch. Are there any downsides to using the built in switch on the phones or should we patch in the second lines to each office for the phone as dedicated cat5?
There's several down-sides imho. The least of which is... if the phone goes down/gets rebooted... the PC will be disconnected. Additionally, if you get into provisioning & VLANs, there sometimes can be a headache to make sure the VoIP data is on the proper vlan... separate from the PC's vlan. Bandwidth typically isn't an issue unless the workstation requires a big chunk of bandwidth regularly...
I am of the school of ... "if you need 1 line... run 4. That way when reality hits... you won't have to run additional lines." especially as Cat5 is cheap.
We run all our PCs in our offices with network cables plugged into our phones.
As to whether or not it's a good idea, that depends on the switch built into each phone. What speed does it run at, will it respect VLAN tags if you're using them to separate voice and data traffic, will the switch component go offline if the phone component is rebooted?
For example, we use Mitel phones, and have purchased their "Gigabit ethernet stand" because the built in PC connection only ran at 100Mb. The gigabit stand doesn't disconnect the PC when the phone restarts either - never tested the 100Mb version.
For speed of deployment I would connect your PCs through the phones for now.
When everyone is happy with the VOIP system's performance you can re-do the telephone lines as an additional ethernet jack for each office (or at least the offices that need it - IT folks.)
For long-term use I favor multiple cat5 drops - especially if you've invested in gigabit infrastructure (all the phones I've ever used have been 100Mbps switches). As an added bonus, if one jack goes bad (wonky cable, construction gone wrong, etc.) you still have a chance that the other jack is working, so you can move the user over to the "spare" jack until you can repair the cable problem.
Generally the switches in VoIP phones are exceedingly crappy, especially if you're using bargain phones (Grandstreams, low end Aastras, etc.). I've seen them be as low as 10mbps switches. If you can afford it, I'd run separate cable drops for the PCs. It will save you headaches later.