So I am pretty new to using Alphia India's flight plans. I tried to install using ttools to convert to FSX format and I am not sure where the traffic bgl created by the compiler should go. Can someone please help me with this?

The .bgl files go in your scenery/world/scenery folder. I am not familiar with TT but if you use AIFP, as soon as you point the destination to that folder once, its all done for you.No need to convert anything.

Ok thank you Ian I will let you know if that works.

Ttools is pretty old school. I've been an AI addict since it was first added to FS and I haven't used Ttools in about 10 years. Try AIFP instead, far more functionality.

An AIG schedule is recognized by AIFP which then will automatically download the liveries ("install repaint") that are used in the schedule. The models needed can be found on this AIG webpage:

http://www.alpha-india.net/forums/index.php?topic=23926.0

There are still a few AI models (because of lack of permission from the original author) that cannot be converted to FSX format and legally disseminated. With a little diligence, these models  (if needed) can be converted with Model Converter X (MCX) for personal use.

Is there any freeware AI that is not WoAi? A lot of the packages are really outdated.

  WoAI is just the very tip of the iceberg in freeware AI. So much more available from various sites as Alpha India Group, http://www.flyingcarpet75.com/ , http://fsxaibureau.com/, http://www.juergenbaumbusch.de/, https://jcai.dk/  just to name a few.

My AI are invisible now, I used AIFP but still no luck.

 Then you have installed something incorrectly. Are they actually invisible or not even there? Using the correct model to each repaint and also having the correct aircraft.cfg entry is integral to it all working together. There's so many possibilities with such little information to go with.