Hi chintu
Thanks for your questions.
I hope these answers are useful, and that they will help others as well.
Unfortunately, I cannot see a section where I can store all my websites' files (I actually have so many tiny niche mini sites that it is sometimes hard to manage and keep track them). Currently I put them all in a folder called 'My Websites' but could have been better if I could access everything using the index map.
Anyway, can I add my own custom folders?
As a general answer - yes: you can add your own folders anywhere - and that's what you'd expect to do. What you cannot do (without buying Mind Manager - and I DON'T recommend it anyway) is add new topic to the Map. To get to the folders you add, you just need to click on the partent folder that DOES have a link on the Map. It's not a big deal.
More specifically, you have a number of options here.
Option 1:If you treat each website as a "Project", you could create a separate Project Map (+ folders) for each one (Look under Quick Links -> Projects).
The folders for each Project include a Websites folder.
The advantage of this is that, if there is other information about each site that you want to store, you can keep in the other folders associated with that Project.
The disadvantage for you seems to be that you have a great many websites, so to create a Project for each would likely be unmanagable.
Option 2:If you want to organize your websites by niche, you could use the Niches folders.
Underneath each Niche folder, create your own Websites folder, and store all websites for that niche within that folder.
You won't be able to create an extra topic in the Map for those folders, but you'll still be able access them quickly via the Map.
Option 2:If you just want all your sites in ONE place, listed alphabetically, but you want to get to it from the Map, then use the Extensions facility (Quick Links -> Extensions). You can either put a shortcut in their to where you currently store the websites, or can just move your websites folder into the Extensions folder.
With options 2 or 3, I would recommend creating a single Project (say Niche Websites) so you can store all your other information and records relating to your operations - such site performance information, affiliate program lists, etc. etc.
How do I organize my Favorites in IM Index? I did watch your two videos but couldn't find the info. Maybe missed it

There are two problems with Favourites:
1. If you have a LOT of them, you need to structure them in some way - and that is EXACTLY the general problem of structuring IM information. Do do it right, you need to have the complexity of the IM Index folder structure replicated within you Favourites - and this would be just too much!
2. There is no way of recording why you stored the link, what's important/interesting about it, what you've done with it etc.
If Favourites is used to keep a SMALL number of links that you use on a very regular basis - it works fine. If you try and use it as a "link repository" it becomes a hopeless jumble.
SO: if you find a link that you want to preserve (but aren't going to visit on a regular basis), don't put it in your favourites: find the relevant topic in your A-Z of Internet Marketing and store the link in the URLs files that is already created for you.
It takes more effort, of course, but you do end up with the link in exactly the right place for you to find it when you look under that topic, AND you can add notes about it.
I regularly find links I'd completely forgotten that I'd saved when I open up one of my URLs files for a topic. This does work very well.
Hope that helps.
Regards
Alex