You need to take all required distributions immediately. This means you calculate the distributions as normal for each year required (i.e. the year in which you reached 70 and 1/2 and following years) and take them immediately along with your normal distribution for this year.
The principal penalty for a failure to receive a required minimum distribution is an excise tax equal to 50% of the amount by which the required minimum distribution exceeds the amount actually distributed (i.e., the shortfall for the year). The excise tax may be waived or reduced by the IRS if you establish to the IRS's satisfaction that the missed distributions were due to reasonable error and that reasonable steps are being taken to remedy the shortfall. The IRS gives the following examples, "if the organization that sold an IRA to the taxpayer gave incorrect advice or if the taxpayer made a mistake in using or did not understand the required minimum distribution formula, he or she might request that the tax be excused". Your reasonable cause excuse would be that you were taking additional distributions out of your 401(k) to cover your IRA RMD requirements because of a misunderstanding of the RMD rules (i.e. you thought you added all tax-deferred accounts together). I would make a big issue of the fact that you took 401(k) distributions in excess of what you had too. I would even show the calculations you made that added all the accounts together (i.e. IRA and 401(k)) to determine the 401(k) distribution you took in satisfaction of what you thought were the RMD requirements.
The excise tax first must be paid using Form 5329, which must be filed along with the individual's income tax return for the year the distribution was missed. The taxpayer would attach an explanation of his or her failure to receive the required minimum distribution, showing the reasonableness of the error and the steps taken to correct the error. If the IRS agrees, a refund is sent to the taxpayer.
Accordingly, you are first required to report the underpayment, pay the additional tax and hope the IRS accepts your excuse and gives you a refund. Many taxpayers take the additional distributions and choose not to report or pay the excise tax. By reporting the distributions and paying the tax, you give yourself a chance to avoid the excise tax as well as underpayment penalties and interest (although the IRS may deny your request and apply penalties and interest if they do not like your excuse). By not paying you may avoid the excise tax (for now), penalties and interest, but if the IRS audits and discovers the underpayments, the penalties and interest could be larger. Also, depending on the size of the underpayment, it could be significant enough to extend the statute of limitations from the normal three years to six years.
I would recommend that you properly report the underdistribution and pay the penalty with Form 5329 along with your attached explanation.