u r already very lucky! 呆呆

In quite a lot universities, the boss just applied one year for you in the beginning, then extendeded it one year by one year. Every time when you renew it, you are asked to prepare your files as if it were new one, not mentioned $185 for I-129 and $195 for I-539 dependents paid by you.

Finally on your question, you H1B will be started from the the date you take your job. You will not lose one day for your whole 6 years (Maybe in the last year, you just have an extension of 180 days)

However, do not worry. Most guys started to apply green card at the second year (even at the first year) and got it in 2-3 years.