you can get them from the Marketplace or if you go to the auction house you can search for them and buy them from other users, that can be cheaper sometimes
mostly just cosmetic things like changing the breeds and genes, there's scrolls to hatch your eggs early and to change their eye types (you can see the different eyes in the morphology page I sent, too)
oh there's also items that do effect stats but that's purely for battling in the coliseum and the stats don't get passed on to offspring, but i don't do much coli fighting so I don't have much advice there
You can get a small amount of gems through gameplay! Mostly through the iron and gilded chests that familiars give when you achieve higher bonding levels
Yeah, what to do really depends on your play style! Broad things to note re: Dragon Economy is that dragons themselves are generally pretty cheap and readily available; you may sometimes have to pay more if you're looking for something really specific but you can get pretty dragons for very little compared to the cost of things like gene scrolls
Which means that if you want to use dragons as a source of income, the easiest way to do that is not to sell pretty dragons for lots of dragon money, but to sell a lot of mediocre dragons for a little bit of dragon money each. This is because when you "exalt" a dragon (i.e. remove it from the website as an interactive item) you get some treasure back
so people who go the coliseum route for making money will often train dragons to level 7 and then exalt them, either breeding their own for the purpose or buying up cheap ones.
you don't have to go that route, though, if you don't want to run a hatchling mill. there are also the fairgrounds games and you can grind the coliseum for item drops to either use or resell
just one more tip though, if you have clothes or familiars you can put on your dragons, having one or more of those attached to the dragon prevents you from exalting the dragon, which is nice in case you click the wrong button (it's happened to us all)
you can also cycle through familiars even if you don't have enough dragons for all of them! (it takes more time, but also nets more treasure and eventually gems)
You can go to this page and try on different genes for dragons