Just to clarify, because there seem to be several things happening and being talked about--and this is just my understanding from hanging around on AW
1. It's a bad idea to be subbing to agents and publishers at the same time. If an agent decides to sign you, they'll want to sub to the same publishers, but that bridge will already have been burned. And a sub from an agent will (generally) have more cred than an unsolicited one from a random author, so you'll have shot yourself in the foot.
2. If you sub directly to a publisher and you get an offer, agents will be the exact opposite of reluctant to take you on. You've done all the subbing work for them, now they just have to negotiate the contract. As mentioned above, query with "offer in hand" or something in the subject line.
3. If you have an offer, should you bother with an agent? Oh, hellz yes. IMO, of course. Agents know a lot more about the industry, how to negotiate, when to negotiate, what to negotiate, etc. 85% of more money is better than 100% of less money.