I am confused on when to use Dobre and when to use Dobry (missing accent marks because my keyboard wont load them) any advice?
Wait for the next skills where the grammar (genders and cases) are taught. Just remember it is Dobrý večer/den and Dobré ráno and Dobrou noc until then.
I've read that the first syllable is stressed in Czech words. In dobry, however, I hear that the second is stressed. Should it be pronounced like that, if yes, what's the rule behind it?
"Officially," from what I understand, in Czech the stress is always on the first syllable. However, in practice, when there is a long vowel in another syllable, the stress seems to shift to the syllable with the long vowel. One of the CZ natives may be able to give you a more authoritative explanation.
First we have to agree on what "stress" is. It is actually not such a simple problem. See https://fonetika.ff.cuni.cz/en/czech-phonetics/ and listen to those recordings there and read the descriptions. The main information is Word stress in Czech is fixed on the first syllable of the stress group, and it is independent of vowel quality and quantity, as well as the morphological structure of the word
The acoustic manifestation of Czech lexical stress is very interesting. Unlike in many languages, the stressed syllable is not associated with typical signs of prominence. Unstressed syllables are often higher, louder and longer than stressed ones. More specifically, it seems to be the post-stressed syllable which tends to be, speaking strictly objectively (acoustically), more prominent.