Perhaps others will follow with more or better advice, but from here, (which isn't a very good 'view'), this is how I see it.
You have no choice but to run the shingles as you normally would. Beings that the roof on the Main House is already done, it may not be possible to retro the NEW roof as if they were both done at the same time. In order to have that 'same roof look', you may have to redo the roof on the Main House too.
Now, the roof on the Main House probably doesn't have to be done BUT, for future reference, assuming it will need to be done, they be sure to install the roof on the Addition so it will line up with the Main House's roof when you do it later on. See what I mean? Then again, maybe I'm not envisioning the job (as you already said, it's a bit confusing.)
Maybe you can come back w/more info. Tell 'us' what type of roof is on the main house AND the addition. Tell us which way the roof 'runs' on both structures. Tell us if there are any 'valleys' too. At the same time, it may pay to find a friend-of-a-friend that knows roofing to give you some advice. Heck, for the $$$ you're saving, offer $50 for their advice. That's a bit more expensive than the advice you're getting here. (LOL)