What do you mean by `second tray', the manual paper feed or a real second tray that you've put below the printer?
If it is the former, the solution should be very easy: Select Print from the File menu and then select Paper Feed from the popup menu below the paper orientation and scale fields. There, you have to switch from Automatic to a specific tray. In case of my laser printer, it shows Automatic, Tray 1, Tray 2, Tray 3, and various other Trays which are grayed out (because they haven't been installed) and Tray 1 (Manual) for the manual paper feed. The names may vary, but you should see options like those.
If you want to use the manual paper feed, then select the appropriate tray (e. g. Tray 1 (Manual) in my case.
If you have indeed installed a separate paper tray which is installed `below the printer' and that cassette is grayed out, you need to manually turn it on. I'll give you instructions if that is the case.