Yes, you can queue a project, including just an In/Out point to AME and continue working in Premiere. This will create a copy of your project at the time you send it over to AME and nothing you do in Premiere after will affect the current AME queue. Click the Export tab at the top-left of Premiere or hit Ctrl/Cmd + M and instead of clicking the blue "Export" button, click the button to the left that says "Send to Media Encoder."
After re-reading your question, I'm wondering if you're asking about using AME to do background rendering on a specific portion of your timeline while you continue working. If that's what you're asking, then no, Premiere doesn't support background rendering, and AME can't be configured to do anything directly to your timeline.