I think it's great that you're cross training!
Learning karate will definately help your atemi and it will also help your fellow students practicing against stronger attacks. I think the key to keeping them separate is your mind set. You might try this; when you're doing karate, keep your mouth shut (don't clinch though) and take shorter breaths.
When you practice aikido, take a deep breaths and have a big smile on your face!!
I have found it very hard to do karate or judo with a big smile on my face, but aikido works well with this!