With regards to merging two logo files, I am assuming that you're talking about bitmap images. Farm Works itself will not merge these images, the program will take a single image and use it as a logo on any maps that you print out. The best suggestion that I would have would be to try a program such as Paintbrush to merge the images.
If you go to the File menu and choose Preferences then select User Info, you will go to the User Information box where you will be able to use the Browse button to select the file that contains your logo. Remember that the logo will need to be in a bitmap (.bmp) format and should be 300 x 150 pixels.