well, the wierd face/masking issue... try lowering the opacity of the masked portion to 50%..or until it looks better. also..click on the keyframe bar..zoom in..thn start placing your mask beacon things...then you can do all sorts of shapes etc.

i am slightly confused on the audio part i'm afraid...butif i interpretated it correctly..you simply just need to right click and insert new audio and have a couple of layers of audio so you are free to edit the desired track with out bothering the others.

also, regarding rendering settings:

save as type: MainConcept AVC/AAC (*.mp4)

Video tab:

Frame size - (custom Frame size)
Width 1280
Lenght 720

Profile - Baseline

Frame rate: 29.970000

(tick "allow source to adjust timeline")

Pixel aspect ratio: 1.0000

(click on "variable bit rate" and tick "two pass")

Maximum (BPS): 4,000,000
Average (BPS): 2,000,000

Audio tab:

Sample rate (hz): 48,000
Bit rate (bps): 6,000

Project tab:

Video rendering quality: Best