Lots of options. Some common solutions;
Router a channel on top of rafters and such to contain your wiring before you put the top on.
If you are using sips for roof they can contain wiring in channels or imbedded pvc pipe.
Where you exit timber tops to the fixtures there are wood look alike plastic channels for containing the wiring to the ceiling fixture(s).
(so you dont have to fabricate boxes)
In any case you are looking at some very careful prior planning so the wiring just kinda falls into place.
You may want to consider X10 so you have wireless dimmer control and such from a hand held remote and/or a central control location.