What you are seeing is ok. The surface mount parts are always red in this case because pads only exist for these part on the top layer which is red by default. If you were to set the opposite property for one of your surface mount parts the part would be mirrored and you would only see the pads for this part in blue.
The through holes have pads on both the top and bottom layers so when you select the Top layer the pads appear red and when the bottom is selected the pads are blue. Since all of your routing is done on the top layer your connection between parts are made by routing traces between pads using the freestyle routing tool, just as you have started to do on this layout.
Through holes are easy enough to make connections to since you can start and end traces from any layer to make connections. Once you start routing connections to surface mount parts on differenet layers you will need to start using vias. Please review the forum post on how to route vias for more information.