IRS and the states do a really good job assessing these penalties correctly they are determined by the date the payment is made and when the return is filed. I have always told the client  It will be about $xxx.yy  and you will get a bill. If it off too much, give me a all.

Just file the return and pay the tax. Wait for the letter. Even if you jump through all the hoops to get it right you do not know how long the agency takes to process. There is almost always a difference and a LETTER. I hate LETTERS, but I expect LETTERS for this one.\

 
Get the return filed as quickly as possible.,