Media Encoder has a presets panel. Look in the list for what you intend to send the video to. If it's Vimeo or YouTube for example, there are presets for those. There's a huge drop down menu in the preset column of the Queue panel.
It's a good question about Media Encoder and subscription. If you end up just subscribing to Animate, I'm not sure whether you get the later versions of Media Encoder. You would get access to Flash Pro CS6, and that came with an earlier version of Media Encoder that would do what you need anyway.
If you are being paid for the work you do you only have to find $50 per month of that income to get the full CC subscription. It is sometimes handy to have access to Photoshop, Illustrator, Premiere, After Effects, and so on.
Disclaimer: I'm Adobe Community Professional, as well as being MVP. I personally don't have to pay the $50. But I'm pretty sure I would.