How to inform conference organizers about your legal name I am in the following situation. I have a name I prefer to use for personal reasons but the name on my passport is different. 

If I apply for travel support for a conference, the recommendation letters will be for the preferred name but the invitation letter for visa, if I am to use it, should be for the legal name. What is the protocol for informing the organizers about this discrepancy?

In my previous experience, when my preferred name and my legal name were the same the organizers issued the letter for my preferred name without checking whether it is my legal name so action from my side must be necessary.

When you apply, there is a form; should I simply fill out the name field like "Preferred Name (legal name: Legal Name)"?
Your situation isn't uncommon. In particular, many women prefer to use their birth name rather than their married name for reasons of continuity, etc. Some people need to use an alias for various security and/or political reasons. 

Just include a note explaining the situation as you have here. If you are asked, you might offer to provide a photocopy of the first page of your passport for verification. But only if asked.