I was checking out some flamenco videos and the guys tend to use their thumb a lot for fast picking. Why and how do you perfect this,,

Also When they strum on upstrokes in particular they use the index finger which resting on the bottom string...bad technique or does this help?..
Flamenco techniques are very varied from player to player, all that matters is sound and efficiency of it.

The reason why thumbs are used VERY frequently is for the 'fat' tone and also volume. Historically, the flamenco guitar's role was only to accompany singers and dancers, who can get quite loud. Thus techniques were needed to allow the guitar to be heard.

Thumb speed isn't everything, try to focus on getting that fat tone. As with any other scales, thumb scales require practice similarly. Start slow and build u as with any other technique, no magic to it.

I don't understand your second question though. Either way, strumming up and downstrokes with the index is very common in flamenco technique.
Not alternate picking. But alzapua is a very interesting flamenco guitar technique which uses single notes combined with up and downstrokes of a few strings, resulting in this unique sound I can't describe. Search on it.