What smells affected Isabel? In other words, what smells reminded her of something?

Isabel smells a lot of different things throughout Chains.  Anderson does a nice job of hitting that sense for readers.  It's the second part of the question that greatly focuses this question.  The smell has to trigger some kind of memory in Isabel.  
The first time that a smell triggers a memory for Isabel is in chapter nine.  She has been asked to wait upon Master Lockton and his friends while they discuss how to best bribe Patriot soldiers.  Isabel is asked to bring the men some jam at one point.  As the men begin spreading the apricot jam, Isabel tells readers that the smell of apricots reminds her of the orchards near Miss Mary's house.  That's a nice memory for Isabel.  
The smell of rose-scented soap is not a nice memory for Isabel though.  That smell reminds her of Madam Lockton.  
Near the end of the book, Isabel tells us that the smell of fresh-cut hay reminds her of home.