There are many insightful posts on this subject. I agree with the poster who stated to always allow a day or two between giving heartworm and flea medication, as that will allow you to hopefully trace any side effects to the respective medications, should they occur.
I have given Comfortis and yes, it did indeed create less than stellar stools for my BC, who passed away a few years ago. Here is the post which really concerned me (read: responses) regarding Comfortis:
Comfortis the flea-killing wonder-drug, and the general state of flea drug resistance | petMD
I have only needed to give flea medication once in 3 years and used Advantage without any issues at all. The heartworm preventative I am currently using is Heartgard (not the Plus). I don't feel that I run any risk of my dog contracting Roundworms (he doesn't eat random rodents) or Hookworms, as he lives in a condo. I may change my mind on this, however, that is what we will do for the next 5 months. He previously was on Interceptor with no issues.
I dislike combo drugs, such as Trifexis, for the reason that I don't see any need to consistently give flea medication, unless I see a flea.