With the advent of biscuit joinery we may do less dowel work that we once did, but there is still the need to get that round stick of wood into a hole. When drilling the holes, use a brad tip bit, it will cut the grain cleaner on the walls of the hole and allow for a better fit with the dowel. Check your dowels, some may have dried into an oval rather than a round shape.
To line up dowel holes on opposite pieces of a joint, use dowel centres as shown in the photo. They come in sized to fit exactly into the dowel holes, and them make a line-up mark at the centre of the hole in the opposite piece.
When lining up a lot of dowels at one time, like for a ladder, barely insert them into the first hole so that they all wobble a bit and are at various heights. That will let you wiggle them into place one at a time as the opposite piece is brought slowly down.