Greetings!
You have a good question there.... I personal have never seen anyone here post anything about using a series of bits to create a special molding. I have seen this done on a couple of the PBS woodworking shows but they never really go into much detail either.
I generally stay with very simple designs and just sketch the idea I have then try to figure out what bits will make that shape and will I have to stack several pieces of wood together to get the profile or can I do it cut it out of one piece...... Will the wood pieces be big enough to hold and route or do I have to make up special "tunnels" to work safely.
I'm sure that was not much help to you but maybe someone can give us all a detailed posting....
Now for the second question, if you are using a fence you will want to isolate the bearing (adjust the fence so the bearing doesn't touch the work piece). The fence is taking the place of the bearing.......
Ed