To load multiple aperture files along with gerbers, goto menu: File | Import | Autoload... Here you can select the directory where the gerbers & apertures are located, and then click next to assign the correct aperture list to use with each gerber file (in most cases Fab It! will do this automatically). The press next to instantly begin importing.
If the apertures are not appearing, this most likely means that Fab It! does not have an "Aperture Wizard Template" (AWT) file. Each PCB layout tool has their own unique aperture file format that output with their gerbers and they usually change the parameters of their aperture files with each version, this results in thousands of different aperture list formats out there in the world. Luckily Fab It! comes with many AWT files and can handle 90% of these aperture files out-of-the-box. For the few exceptions, we have created an "Aperture Rules Editor" which allows you to easily create a AWT for your particular aperture file type. Once you have created the AWT Fab It! will always be able to "automatically" detect those aperture files. Goto menu: Setup | Aperture Rules Editor... to create an AWT.
Note: You may also send us your Gerbers & Aperture Lists (for any files that don't load-in), and we'll create the AWT for you within one business day - FREE of Charge. Zip up all files and open a Support Ticket (make sure to include your zipped file).