1. When you try to form a pair artificially, both fish should be adults and well conditioned. "Naturally" would be when you have group of suitable breeders together and the fish pick their mates without the aquarium keeper playing match maker.
2. The regular JD should be the smaller one. The male EBJD and a female regular JD is usually easier. If you have a good regular male who does not seem aggressive and want to breed more than fight, you can try the reverse cross, but because the male is so much more powerful than the female, it's risky and you have to be there watching. Her eggs are likely to b e smaller, and have a low hatch rate. (You could also try pairing off a EBJD with a gold JD.) If you seem to have a really healthy EBJD strain, you could try mating them. Some day it may just work for someone. As it is, the pure EB fry seem too weak and after a period of development, die in the egg.
3. Whether it's a regular or EB, females have a concentration of blue flecks on their gill plates and few flecks anywhere else. Males are the reverse and have blue flecks all over.
I've bred electric blue, regular ,and gold Jack Dempseys. If you follow your plan, it's not likely you will get the percentage you expect. When you cross a male EB with a regular female, the regular female either carries two genes for regular or one for blue and one for regular. (Forgetting about the gold morph for a while.) All of the fry from regular female with two genes for normal will have one blue gene from their father and one blue gene from their mother. If you cross (inbreed/line breed) two siblings, one fourth will get two regular genes, one fourth will get two blue genes. One forth will get a blue gene from the mother and regular gene from the father. One fourth will get a regular gene from the mother and a blue gene from the father. The actual genetics in the fish is the genotype. With recessive genes, records are important. Three fourths of the spawn will look like regular jack dempseys but half of the spawn, looking just like the one fourth that really are regular JD's will carry one hidden gene for blue. Some of these fish end up being sold as regular JD's and so it is not impossible that your first mating would result in 50% regular (but carrying a recessive for blue) and 50% blue. Since blues are weaker from the start, the percentage of blues will be lower than that.
As to golds, that I find confusing even though I have bred them. The genetics of golds is something that you want to grab Gregor Mendel by his cassock and say, "Explain this!" When breeding blues, golds sometimes show up, but as far as I have seen, not the other way. Whatever is happening is so strange that if someone else had the opposite happen, I would not be surprised at all, and not any less confused.
There is no real controversy about the electric blues being a mutation or a hybrid. They were originally reported as a mutation. They are a mutation. The genetics of dealing with the blues is typical of a mutation and none of the variations or partial inheritance you would expect with a cross happens at all. Someone visiting the first breeders facility noticed some other kind of fish there, put two and two together and came up with twenty two and then squared that to the power of gossip. I have known that particular guy since the mid 80's and I have learned if he said the sun would rise tomorrow, to check the paper for the time of the solar eclipse.