Bonus & commission income is averaged over a 2 year period. So if you are paid W-2'd income for 2 years, and if it is all bonuses & commissions, then a 2-year average of bonus income would be put into one category, and a 2-year average of commission income in the other, and then added together. It also has to be analyzed to see if there was a major increase/decrease in either category from one year to the next, as if there is a severe change it may result it only the most recent year being used or not being used.
1099 income is self-employment income like Alex laid out as it is reported to Schedule C of your personal tax returns, and most lenders require 2 years of self-employment income. So if you are paid 1099'd income, and the composite of your 1099 income is bonuses & commissions, it is all just reported as income - there is no further analysis to determine if it was per contract income, commission income, hourly rate income, a 1 time payment of income, etc... it's just simply self-employment income. The income is analyzed like Alex indicated, your gross income minus any actual expenses you claim on your Schedule C.