Alternate picking has been covered in the other answer, but 'economy' picking needs explanation.
When the note being played is on, for example, the third (G) string , and the following note will be on the 2nd (B) string, it's sometimes better to play the 3rd string with a downstroke, effectively moving in the direction of the string that next note is played on.
If the 3rd string note is followed by a note on the fourth (D) string, then that 3rd string would be played with an upstroke, the pick moving in the direction of the next string (4th, D) to be played.
In some cases, it's necessary, using this method, to jump over the string played second - as in when the next note after is on the (in this scenario) third string.
It all sounds quite complicated, and I remember, many years ago, working out note for note which pick direction to use. Not easy, but the concept has stayed with me, and still works, alongside alternate picking when needed. It's a bit like running - after a while, it becomes so natural you don't think about it - and if you do, you fall over...
Another very useful method is hybrid picking where pick and some fingers get used. To me this is very useful, as the pick can often stay on one string, while another is played, often alternately, with a finger. Hold the pick between thumb and index, which leaves the three other fingers free to do all sorts of clever things!
In direct answer to your question - the bottom E (fat 6) is generally played using a downstroke. It's often playing a root note, and on the beat, and the next note is often on a thinner string, so playing it with an upstroke becomes counterproductive. When you used your thumb for the same, I expect that moved towards the floor - a downstroke.