I think you've got a pretty neat little setup there already...
Personally, I'd make me a hang on the wall type pen- about 2x6x2, right inside your little 'shelf' on the outside.. Cut out a single board, and make a pop door through the wall-- fence in that outside shelf-- and bam- you have an elevated breeding pen... If you want it double decker, do the same thing under it, but since you were worried about floor space on your layer hens- then I'd just leave that hang on pen there... YOu know, the interesting thing about chicken houses, is the chickens only use the floor, and the corners (for roosting), they don't actually use the walls

So, by putting the 'hang on' type small breeder, or grower type pens, with a sliding pop door to an outside run (either on the ground, or elevated (with a ladder) you're actually utilizing the whole henhouse...
To go one step further, build two pens side by side, and make your outside shelf twice as big with an addition. Make a slide out divider b/w each pen on the inside, as well as the outside (with a door access)- so you'll be able to remove the dividers and make it all one pen. By putting a divider on both the inside and outside, you'll be able to make both inside pens one, both outside pens one, all 4 pens one, or the best one *if chicken math takes over*- 4 individual pens each with shelter.
if you're getting as much snow and cold as I would suspect you to-- either outside runs with tops need to be used, or just plain keep the birds inside... Regardless- I think that's what I would do (and actually plan to in our chicken house)