Re: Sometimes I use the native Android app to add contacts too.
Be careful which account you create those contacts in.
If Aqua Mail then Android will call Aqua to sync those new contacts to the server -- since that's what you're telling it to do -- and then Aqua Mail will also sync from server to phone.
The check for "is sync enabled, if not, do not sync from server to phone" is done, and I'm about to post a new build.