Unlike conventional armed forces, there is no centralised command structure.

Majority of these groups have been formed initially using local militias. That’s why you get names such as “Abdullah Brigade” (for e.g) and under leadership of that person you get other smaller leaders who all know each other because they belong to the same local region.

Some of these groups are (and were) quite closely knit and that’s why it was so difficult to fight them and the level of friendly fire was also rather limited.

HOWEVER, ISIS changed this because of being made up from fighters from all over the world. And this is precisely why ISIS failed to keep hold of territory, had vast amount of friendly fire incidents, mass amount of overall deaths as well as being involved in "war crimes" which we have no opportunity to convict them of as there is a lack of evidence.

Although, there is documentary evidence such as videos, and instructions given by individuals such as Baghdadi, it is still difficult to pin point exactly who is part of ISIS and who was previously fighting for ISIS. This is what makes terror groups like ISIS much more difficult to fight as its members are hidden in plain sight.

I should also point out to the fact that groups such as Al Qaeda are extremely well controlled as was demonstrated by the raid which killed Osama. Considerable amount of data was recovered from the compound of Osama which included lists of active members as well as past supporters who provided financial and logistical support.

In addition, specifically in terms of your question of how logistics works with these groups the simple answer is that it doesn’t. Supply lines are corrupted and this was (and still remains) one of the key criticisms against the American supply of groups in the region. Weapons you supply to “friendly” groups have made their way into the hands of ISIS over and over again.