Is the complication that your service only offers separate RMDs from each account, and you cannot specify some other combination? Doesn’t seem likely that one account would be drained unless you are aggregating more of your total RMD to that account.
I’m taking my total RMD from the smaller of two IRA accounts to close it out first and then continue with the remaining account. The smaller account will soon be less in value than the total RMD and the actual value of that account is not known until the trade date. The automatic RMD service specifies withdrawal amounts that will take place on a future date. It looks like I may have to manually close out the smaller IRA and then calculate the amount to withdraw from the larger account. The second withdrawal could be either manual or automatic.
I was disappointed to learn that my automatic RMD service does not appear to adjust to any manual withdrawals taken before the scheduled withdrawals.
There may be valid reasons for the way things are done. After setting up the automatic RMD you receive a formal RMD Service Agreement and a formal RMD Confirmation Summary. It looks like there are times when the automatic RMD needs to be updated manually. There is also some complexity in these services as withdrawals can be taken on a quarterly, semiannual, or annual basis.