An individual is under 59-1/2, has 2 IRAs and wants to take substantially equal payments. Can the individual determine the amount of the substantially equal payments based on the value of only one of those accounts or must both accounts be aggregated to determine the amount he must take?

According to PLR 9050030, the two accounts don't have to be combined. Here's a quote from question 219 in the 1999 edition of Tax Facts 1 regarding distributions that might be of help.

"Individual retirement plans do not have to be aggregated for purposes of calculating these payments. If a taxpayer owns more than one IRA, any combination of the taxpayer's IRAs may be taken into account in determining the distributions by aggregating the account balances of those IRAs. However, a portion of one or more of the IRAs may not be excluded in order to limit the periodic payment to a predetermined amount."

In other words, you can base distributions on one of the IRAs, but you can't use a fraction of the second IRA in order to come up with a desired income amount.

Hope this is of help to you.