You really want them to be outside for a more permant run. The smell
would get really icky inside. Work on setting up a coop and pen
outside. The kennel run sounds like a great idea. I took my old
storage shed and transformed it into a coop and added about 100 foot
of wire around it to make a pen with enough space left to make the
gate. I spent a few more dollers at lowes for the hinges and some
more nails and another roll of pen wire to make the gate and go around
the pen one more time to make the height about 6 feet or better.
Chickens can fly little short flights. Unless you plan on clipping
their wings you need to make your pen high enough so that your birds
dont fly out.