Ellis Amdur has some interesting suggestions for ways to incorporate atemi awareness into aikido training. His ideas can be found in a chapter of his book Dueling with O Sensei. Some chapters are available online, but I'm not sure if the one that focuses on atemi is; you might have to order the book (available at koryu.com or at Ellis's website, ellisamdur.com). For an aikidoka, it's not a bad book to have on the shelf anyway.
David Sims
"Cuius testiculos habes, habeas cardia et cerebellum." - Terry Pratchet
My opinion is, in all likelihood, worth exactly what you are paying for it.