Ok. So first off:
I used footage that was 720p (1280×720, of course) with *.mp4 format that was only about 3 mins long.
Ok, so after finishing up my project in After Effects, I decided to output composition in H.264, with 'High' Profile, 5.1, using CBR of 8Mbps.
When it was finished, of course I was happy that movie was small yet had same quality, but had some random flickering issues throughout the movie (you know, where it looks like it clipped off a bit here and there in like a split second). I tried adjusting format settings (going from CBR to VBR or changing encoding quality rate to like 16Mbps..still no luck.
I was about to scream and throw my laptop out the window! I read all these forums and posts, telling me possibilities ranging from my PC to my movie to even my effects..yada yada yada..ahhh!!!
So I tried something. I said to myself..let's see what Adobe Premiere Pro would do for me. So I imported that same 'flickering' movie and decided to 'Render Entire Work Area' (I'm not even sure this does anything..so just be patient, I'm a noob 
). I played preview and I was amazed that all the flickering was gone. OK...wow..great! So now comes the real test.
I decided to export with H.264 with a preset of Youtube 720p HD 29.97 format. Nope, didn't work..
. I was about to give up...but then I thought...WTH..let's try matching sequence settings. See screen shot below
So after doing that, guess what...no flicking! And the quality is still good! But, there's a con (of course). It's a little bigger. But it's doable.
I guess from now on, I'll upload footage first to APremiere Pro, render it there, and then try and see what happens..more to follow....