Now, should I run all wire from the service entry to the sub boxes in conduit?
You might want to check local codes for that. Maybe find a friend who does electrical work or a friend of a friend. Just start asking around. Don't bother trying to figure it out, it seems like every town is different.
Then too, depending on what you get done, you may be forced to hire it out. If what you do requires to have the power shut off, PP&L will not turn it back on without a certified electrician having done the work. My last box work I simply hired out. It really wasn't all that bad. I moved the entire service. (well, paid to have it moved).
Recently, I wanted to add a box as well, and just fyi, I have SquareD in the house as the main 200A box. For me to replace 3 breakers with tandem's, it was actually less money to buy an entire new Seimens box, w/mains, w/breakers, w/cable to it, and pay to have it put in. SquareD can stuff their boxes/breakers. Wow, have they gone through the roof in the past 10 years. Insane.
Then too, when you go to get the boxes, consider putting in 20s or 40s instead of say a 10 position sub box. The 20s and 40s with main breaker and busses will be half the money of the smaller boxes without. (supply / demand). Makes no sense, I know. Well, a Seimens 40 position main panel cost less than ONE SquareD 20A tandem breaker. Go figure. Just, shop smart. Bigger common stuff is usually cheaper.
I was thinking of putting a sub panel beside the main. Now for the basement sub, will that run from the main service as well?
Mine does not. Mine is a sub off the main service panel using a 50A breaker in the main box.