[Chuose Osemeka]"How do we now this this once simple thing now in Adobe Media Encoder?"
Your ability to export an Alpha channel hasn't changed in AME. You need to determine which codec your using and if that codec supports an Alpha Channel. To enable the Alpha channel look for a drop down menu called "Depth." That drop down will need to be set to 32bit, which denotes your three channels R, G, and B (24bit) + an alpha channel (8bit). You can then bring that file into whatever software and it should act as you'd expect.
[Chuose Osemeka]"Also how does one reduce the size in AME?"
You'll have to be more specific on this. If you're discussing h.264 encoding then you'll need to look at the data rate you're using and whether it's CBR, VBR 1-Pass, or VBR 2-pass. If you're just talking about any given codec...well that's a big discussion. Different codecs encode files differently using different sample methods - ProRes vs DNxHD vs PNG vs Animaton vs DVCPRO. And within a given codec there can be multiple options offered (ProRes Proxy, ProRes LT, ProRes, ProRes HQ, ProRes 444) which will can greatly change the size of your resulting file.