I have font folio 11 downloaded on my computer. When I go onto illustrator every new font I have is in the font menu. I am now trying to work in InDesign but half of my fonts aren't in the list. Some fonts that are poorly done and licenced are in my list, but not the professional ones that I do need. How do I import all of my fonts to the font book in InDesign?
For the time being I will assume that you have fully and properly licensed Font Folio from Adobe.
There are nearly 2500 typefaces in Font Folio 11.
Are you telling us that you actually installed all those typefaces on your computer? How did you do such an installation? Font Folio by itself doesn't have an installer. All it has are directories with font files and some documentation. You need to do the platform-specific font installation (for example, for Windows you right click the .otf files and click “install”).
Assuming that you have installed all these typefaces plus you have other fonts installed, such as those bundled with your operating system, Microsoft Office, and other “poorly done” fonts from elsewhere, you may easily be dealing with 3000 to 5000 typefaces.
Quite frankly, many applications simply cannot easily handle that number of active typefaces at one time. That is why InDesign supports document-specific font directories and why third parties provide font management software. I absolutely cannot imagine having to scroll through a list of fonts that long.
Perhaps you can provide us with some more specifics as to how you have installed these fonts and why you must have them all active at all times?!?