I am charged for fraud under 5000$ by my employer... 2 other guys were included and total money is more than 400,000$ with 100s of transactions. I knew about it all the way and somehow I did about 4 transactions but never took any money from those guys... what punishment I am looking at?

It appears you are not being charged for the entire 400,000, but will you get 4 different charges or will the 4 thefts be included in one charge.
And then what is the actual total of your four thefts. A 4800 dollar theft is treated different than a 48 dollar theft.

Also will there be chances of them finding or at least charging you with more thefts.

Do you have an attorney, and has he talked to the DA
( crown, state, or what the name is there) about a plea deal if you testify against the other parties.

Also don't expect the court to care or believe you did a criminal act and did not take some of the money,