Do I wait until I file my 2009 to pay 10% penalty and additional tax I held or should I send a check now to the IRS. The amount is 10k penalty and I estimate I will owe an additional 6k in fed tax. I'm thinking with this large liability fed's will charge penalty? Not sure - please advise.

If you have already paid tax (including estimated tax and tax withheld) equal to 100% of tax on your 2008 tax return, then you do not need to send any payment now. Pay when you file your tax return on or before April 15, 2010.