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Following the nice online Anatomical Atlas (http://www.ces.csiro.au/biology/fly/flyGlossary.html) tergite 1 and 2 are fused in Acalyptrata but not in any of the other Diptera groups.

Firstly, is that correct?

Then, I understand that part of the litterature refers to the anatomically 6th tergite when discussing the 5th tergite. So how to avoid confusion? E.g. "the 5thvisible tergite - anatomically 6th - is yellow" ?

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In all the modern keys, 5th tergite is ANATOMICALLY 5th tergite, and if the 6th tergite is present, this means anatomically 6th tergite, and nothing else!

When I describe the acalyptrate abdomens (I was the author of certain keys, for instance, in the Manual of Central American Diptera and the forthcoming Manual of Afrotropical Diptera), I always metion numbers of the anatomical tergites: "syntergite 1+2", "tergite 3", "tergite 4", tergite 5", "tergite 6", "tergosternite 7", etc.

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Thanks Valery, that's clear! If one also mentions 'syntergite 1+2' it is also unambiguous.
Now, do you also happen to know in which groups tergite 1+2 are fused? As Acalyptrata probably is a paraphyletic assemblage, it seems unlikely to me that the tergites are fused in all Acalyptrata but not in Calyptrata.

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Louis: it's well visible: the syntergyte is 1.5-2 times as long as the 3rd tergite and bears partly bare area of fusion, etc. I hardly can recall a case, when I had a problem with this.

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Thanks again, Valery, I'll try if I can see this too!