We have an urban yard (about 6100 sq ft) and started with raised garden beds, then a dog kennel. Then we cut down one side of our hedge and opened up about 500 sq ft of yard that was buried under the thing. Then we cut down another side of our hedge and got another 200 sq ft, after doing that it seemed like our garden beds were in the middle of the yard (since so much opened up without the hedgerow) so now we want to move one bed to where the hedge used to be. But first we have to finish the chicken coop! Did I mention we got rid of the dog kennel? Our lab quit chewing stuff up so stays inside while we're at work. We are also going to cut down that last section of hedge probably this summer and replace the whole thing with a cedar fence as it takes up so much less room.
The point is, in my opinion it doesn't matter what you start with as long as EVERYTHING is planned out in advance. You don't want to put up the dog run and then say "OH NO, that was the best place for the vegetable garden!". So figure out exactly what you think you want to do now (including removal of trees, etc.etc. cause that will change your layout), and then decide where the best place for everything is...best light for garden, good drainage and some shade for the chickens, a dog run that won't get too muddy, or whatever your priorities are.
Once all that is done, then start building. :)
In hindsight, we definitely should have replaced our whole hedge with a fence prior to starting the gardening and chickens. Because it is really hard to envision just how much space is opened up once the hedge is removed and now we are finding ourselves wanting to move the garden beds etc...
my 2 cents.