The baby, when it is newborn, can't ride in a Marathon. I know it says they go down to 5 pounds, but anyone who has tried a 5 pounder in an MA will tell you that is a load of hooey. They don't fit. Until they are about 10 pounds. So you need an infant seat, first of all. You might want to get a cheap one and then just move the babe into the MA as soon as it's big enough. Or you might want to get a nice one to use for a while, and have the convenience of not having to keep waking a peacefully sleeping baby.
For your older daughter, she may fit in the MA until it expires, and at six she would be ready for a booster. Or she may not! It depends if she's has a long torso or not. My dd is very long torsoed and she outgrew her MA by height when she was 4.5 and 43 inches tall! But I think that's some kind of a record. My friend's daughter is the same height as my daughter and has a LONG way to go before outgrowing the MA. So it varies. Where are your daughter's shoulders now in relation to the highest harness straps? IF you want her harnessed as long as possible, the best thing to do is get her a Regent. That way you wouldn't be forced in to switching her to a booster before you are comfortable doing so.
As to whether the baby will be able to use a Regent when the MA expires, it totally depends on how big she is. I think any kid under 35 pounds is going to swim in a Regent. Those things are BIG, and meant for older, big kids. Also a kid under 33-35 pounds should still be rearfacing, and the Regent doesn't rearface. I have met some two year olds who are 35 pounds and chunky and fit fine in a Regent. Most don't. It depends on the kid. But 2010 is a long ways away. Three years is a long time in the carseat world. The perfect seat for that soon to be born baby will probably have been designed by then, so just plan to cross that bridge when you come to it!