As with any language there are no fixed rules, however, the main consensus is that the last vowel and occasionally the penultimate vowel are the ones stressed (possibly elongated) in Coptic esp. Bohairic dialect. It has less to do with which vowels (as is the case with many languages), as with the word itself, and also the position of the word within a phrase.
The whole this vowel shouldbe the long one and this is short, is not really an accurate representation of how people speak.