You should fill "Yes". Most  companies do not know much about the visa details. It does not cost them anything if you hire your own lawyer to apply H1B, which is quite different from the EB green card application. Even you ask them to sign some paperwork in your H1B application, I believe it won't be an issue as long as you are a good employee. On the website of the company I work for, it specifically says: Do not support visa applicaiton but they only mean financially.