I know if your adrenals are shot that has a negative impact on your thyroid function, but I also read if you take thyroid supplements (i.e.armour thyroid) with adrenal fatigue that can further deplete the adrenals? Whats the link there?

There are a couple of things that can contribute to the adrenal crashing.  One is the increased clearance of cortisol putting more stress on the adrenals to maintain cortisol levels.  And by increasing the metabolic demand on the body.

Also if bacteria "supress" the thyroid, is that just the gland, or the hormone? If someone took thyroid supplement like armour thyroid, would the bad bacteria suppress that as well, or is it just the gland?

I don't know what bacteria you are referring to.