You don't need to delete fonts manually in the .UIS file, but if you do things correctly it should work fine. You need to have a different skin applied though when making the changes.
Are you saying you are adding a new font inside SKS 8 but cannot use it anywhere when using the font drop down list in SKS 8? If so, sounds like you may have corrupted your .UIS file. When you remove fonts manually you need to keep them in numeric order. In other words, if you have Font 1 - 10 in the .UIS file, and you remove font #2, 6 and 8, you need to re-number the fonts as 1-7 thus keeping the correct sequence.
Hope this helps, but a word of advice, do not mess with the code in the .UIS file unless you really know what you are doing. 
