Is this another problem with intercessory prayer or with whether the saints in heaven are "dead"?
The saints (all those who are saved) are very much alive in heaven.
What makes you think they know what is going on earth?
The only prayer stated in scripture by any saints in heaven are those who are martyred by the Anti-Christ, and they aren't praying for anyone, they are seeking justice. (Rev.6:9-10) on the one who had killed them-Rome (Rev.17:5-6)