Housing

How to house your birds is not a difficult question - but there are many answers, and the answer is ultimately based on personal preference, especially if you intend on breeding.
For active birds that need room for flight, cages that are longer than they are tall are best because they offer the most flight room. Avoid placing too many distractions in the cage - or placing so many perches that birds can easily hop from one to the other rather than fly.

Colony vs. Individual Housing

In colony breeding, all of the birds are placed in one large aviary and allowed to breed at will with partners they select. In individual breeding, pairs are selected by the owner and placed in breeding cages with no other birds. There is really no 'best' method to breed - there are many different reasons for breeding individually, and many reasons for breeding colony. There are also pros and cons to each. What you have to do is evaluate each method and decide which is best for you.
I practice individual breeding and do not colony breed. The reason I do not colony breed is because I am breeding with very specific intentions, and it is important for me to know the exact genetics/heritage of my offspring. I house my breeding pairs individually in cages that measure 24"x24"x24" at the very least. The majority of my breeding pairs are in 36"x36"x84" flight cages. The finches are housed in their own free flight aviary which is 10'x30'.

Perches

I prefer to use natural branches when possible though I do of course use dowel perches as well. I feel that natural branches tend to be better at keeping the nails filed down, and the birds just seem to enjoy them more, and heck, they're free!
Refer to an avian safe tree list when cutting branches for use in an aviary. For example, Cedar trees produce oils which are toxic to the birds. Generally speaking many fruiting trees and oaks are safe. I recommend providing a variety of widths in the perches to keep the feet exercised.

Breeding Flights

Finch Aviary