Funds of this nature can be used as either assets or income, but not both. Since I don't know your over all profile, I can't answer which would be best for you. However, If these funds are required to be used towards your down payment and closing costs, then they will be looked at as income by underwriting.
If so, this is how you need to proceed: FHA/VA/FANNIE MAE guidelines are that all large deposits must be sourced. That said, if you recently liquated some stocks and placed them in your checking account, underwriting will require 1.) a copy of your most recent stock/mutual fund/retirement statement; 2.) a copy of the check and/or check stub you received from the liquidation of your stocks; and (3) your most recent bank statement that you deposited the funds into. That simple.