It's good to have glazed windows(top hinged or static) in the coop for daylight infiltration for when it's rainy or windy outside, as they may not want to be out in the run portion of the coop during those times.
It also helps them to go into coop to roost at dusk.
Usually when you first put chicks outside, you keep them in the coop only for a few days to a week to 'home' them to the safest and snuggest place for them to be, and where you want them to return to sleep at night. Then let them out into the run. But they don't like 'new things', it's why we call people who are afraid 'chickens', and can take some time and encouragement and/or manipulation to get help them acclimate to their new housing.
Those tiny coops can be hard to manage, adding some ventilation in the coop wall under the run roof can much improve the environment inside the coop.
The roosts and nests are at the same level and can cause problem with sleeping in nests(and thus poopy eggs), here's a great modification of a tiny coop that very nicely addresses that issue in particular that you might want to consider:
http://www.backyardchickens.com/t/1134399/help-hens-roosting-in-nest-boxes/10#post_17749535