There are places on the application for you to indicate that your mother is deceased, that you have n siblings (some applicants count half sibs as sibs so do so if applicable), that you paid for x% of college with loans, and how many hours you worked at at what jobs while in college. And AMCAS will give you an "EO" designation based on your parents education and employment. So, this will all be there for an adcom that wishes to make a holistic assessment of your application.
To anyone wondering about disadvantaged:
"Disadvantaged" usually means that your upbringing from 0-18 put you in a situation where you were disadvantaged when you got to college compared to other college students due to substandard k-12 schools, parents who had no experience with higher education or who did not speak English, a impoverished environment (inner city or rural) and/or poverty. Poverty pretty much has to be part of the mix. You could be stuck in a rural area with crappy schools and no alternative but if your parents have professional degrees and are pulling down a six figure incomes, you could end up with adcoms labeling you as a whiner and being more harsh than they would be otherwise.