You put newborns in the main stroller lying flat. Then toddler seat clips on the front for bigger kid. It's really up to you as to when you change them over, but there's not a whole lot of room in this position for the baby - once they get a bit of chub on them it's not very comfy!
Once P got to about 4 months old she HATED lying underneath, so even though she wasn't able to sit yet we moved the doubles kit to the back and reclined it (it has zippers down each side).
Once you are at that stage, as Sarah said, put bigger kid in the main part of the stroller and remove the adaptors from the doubles kit then clip it on the back. Smaller kid goes in next on the back.
IRT bags, when the doubles kit is on the front you can just use it the way you normally would (although I have a dash so I never hang anything on the handle because that's my breaking system). When the doubles kit's on the back, bags just don't work! I found I could take a smaller bag with essentials (1 nappy, wipes, drinks & food) in the basket underneath and the nappy bag just stayed in the car (or at home if we were just going for a walk).

In any case, you have to make sure you have the weightiest child in the front, so in the doubles kit if it's stuck to the front or in the main stroller if the doubles kit is on the back. I have experienced the stroller tipping backwards when I had too much weight in there (fortunately not a child, LOL! The stroller was full of stuff at the back and nothing in the front) so you do need to be mindful of this.