Hi Asim,
It is good to start planning well in advance and to get all the documents as per the requirements.
As per your questions I could answer them but i could be wrong. It is better to get a professional advise as i am new to the forum but have been following other forums from since few years .
1) applicant got her 309 visa with help of an immigration agent. He got the immi account through which she got her visa. Now, if we decide to apply the subclass 100, can we do it ourself? Do we need to create a new immi account or it will go through the same immi account??
If you are applying by yourself you will need to create a new immi account as the agent will not provide you the details unless you know the person personally. I am not sure if once you create a new account and write to immigration to request the previous application to appear on your current account.
2) we submitted Form 888 with our sublcass 309 application, will it be used for subclass 100 too? What if we want to use different Form 888 for next stage?
I've read in other forums that The form 888 validity is for 6 weeks only applies for specific circumstances - at least that is how I interpreted the info in the Partner Migration booklet.
3) we had a joint bank account for 309 visa, she is here in Australia now, do we need to have a joint account here too? Also having her on a rental lease as a partner helps? Sharing bills under her name?
Yes you will need to have a joint account here in Australia as well, plus adding her on lease, bills etc. Don't forget to add her on your Emergency contact at your workplace .