How do I send documents to WES if I have graduated from an autonomous college that name is not featured in the list of WES?

When you say Autonomous College, do you mean that the Course is not affiliated to any University?

Ideally Transcript documents need to be issued by the Education Authority, who have issued the Degree Certificate.

Probably you will receive the WES Certificate, with mention that Institution is Non-Recognised. No points awarded.

I guess try with WES, but continue to check with IQAS, though it is time consuming.