Taking 2 primary and later on 2 secondary antibodies derived from different species (or sometimes in case of only antibodies available from one species then with different IgGs) is how I was performing all my immunofluorescence stainings. It is working fine...
Of course! For exemple you can use 2 primary antibody derived from 2 different species( ex. rabbit and mouse) and then the secondary antibody recognizing one the rabbit IgG and one the mouse IgG conjugated with two different fluorofores.