If I cross a naga, then reaper, and then a douglah last, would it be the same as crossing a naga with a douglah, and then finally the reaper as last? I don't fully understand how the heredity works out, help would be appreciated.
No it won't be the same but to be fair even the same cross done twice doesn't guarantee the same result twice. It could be but until a test cross is done we wont know. That or if we already know the alleles of both parent plants so that we can do a punnet square. But that punnet square has to be adjusted for the pepper plant being haploid, diaploid, triploid or whatever pepper genetics are.
It's a bit complicated unless we had more genetic information on the phenotype we want to see. So without that its mostly rng, cross them and hope for the best. Then if you get a good hybrid and if there's a trait that you like to breed into your new hybrid, you cross it again with another plant and hope for the best again. Hopefully all the good traits are passed down into your new three way hybrid
On a more simple level though, breed 1 would be 1/2 Douglah, 1/4 Reaper, 1/4 Naga, while number 2 would be 1/2 Reaper and 1/4 Douglah. Roughly speaking.