Recommendation for mail app that works with smart mailboxes?

I've been trying different mail apps but the problem I keep running into is that I have "smart mailboxes" on my MacBook. If I use some of the apps I've tried, I end up with extra folders for the "smart mailboxes" on MacBook and duplicates of a message. It really makes a mess of things and is confusing.

I'm using a 2011 MacBook on Mavericks, iPhone 4s and iPad 3 on iOS 7. I'm trying to sync my iCloud accounts (I have 2 on one ID) as well as a business account from Go Daddy and an account I monitor on Gmail.

If anyone has any advice on what may be the best app to use for this, I'd appreciate the input. I'm working with the standard Mail app but it's not exactly smooth. I'd like to make this easier and cleaner for the number of accounts I have. Thank you.