Hi. I'm in a similar situation. My husband travels 40% of the time and often works late. We have a 2-story home, too.
Sometimes, I let my toddler watch an episode of Dora or Diego. I don't worry too much about her downstairs alone - I have pretty much toddler-proofed the house, have bolts on all of the doors, and my boxer goes psycho if anyone walks by the house.
She doesn't always want to be downstairs alone, though. So, sometimes I have her read books or do puzzles in her bedroom. When she's feeling particularly needy, she knows that she can come sit right outside the baby's door and that she's not allowed to make a peep or be seen by the baby. In that case, I just make up songs about the both of them and often sing about her not being allowed to make any noise or peek her head into the room. Doesn't always work - there have been times when I've just had to put the baby into bed and let her scream. The crying doesn't last long; I'd say 5-10 minutes tops.
I almost always put the baby down first. Her bedtime is 7:30-8:00 and the toddler's is now 8:00. It depends on how long the afternoon naps last. Oh, I've always been to lazy to do this, but some people have special toys they bring out for the toddler to play with while they're putting the baby down. Just make sure they're only pulled out at those times and that they're ones that won't incite them to noisiness.
Good luck! It's difficult, but eventually they'll be teenagers and go to bed all alone and sleep in to noon.