You do misunderstand. Read my first and last sentences over again.
In a boutique agency, the manuscripts come in one at a time, one client at a time.
When a MS comes in, with agreement signed and everything in place, the agent will call or query all of the publishers she believes will want to see it. For every request for a full, she prepares the ms for either electronic transmission or for snail mail, depending on what the editor wants (90% of the time, it's email). Then it's a waiting game. Meanwhile, she works on another ms from another author.
All while the agent is working on a new author, returns come in from the first author's submissions. These should never be ignored. With email, the agent can simply forward the response, good or bad, to the author or editor. With snail mail, the agent either sends the hard copy letter by email in a jpeg file or sends a hard copy of the response to the author at designated times, usually at the end of the month (emergencies get treated immediately). The agent should also keep track of the publishers who refused a look, so as not to duplicate the effort.
All queries, responses, etc. should be kept in the author's personal file, both electronic and hard copy. This way, the agent can answer any question at any time as to what activity has taken place with that manuscript. It's a good system, because if the author wishes to dismiss the agent, s/he has a complete rundown as to who has seen the manuscript and can relay that info to the new agent.
An agent should have everything ready to send to an editor at any time. Some editors want nothing but the manuscript, others want author bios and/or a synopsis, etc. If the agent is efficient, these items are on her hard drive and she can send them to the editor by return email. All of the above items should be in the agent's possession before any placements are done.
All agents take advantage of opportunistic placements. Sometimes an editor will be transferred to another division and will want to see a manuscript s/he originally refused. A good agent will jump on the opportunity, regardless of what s/he is working on at the time.
Hope that clarifies everything.