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In my writings, I would like to indicate short and long vowels when ambiguities might arise (mainly between nominative/ablative and vocative/adverb). Is there a common/attested way of doing this without having to mark every single long syllable with a macron? I have seen people using â, à, etc. for some words, but I am looking for more systematic rules (which words and which diacritics).
Maybe marking where the accent falls is a better option?
Marking the accent is not particularly helpful for disambiguation. The accent can't tell if populus is "people" or "poplar" and whether a word of the first declension is in the nominative or the ablative. If you want to disambiguate with diacritics, use the macron and the breve.
There is no clear and universal rule to decide when to indicate vowel length, so you have to use your judgement. It depends greatly on your target audience and the medium. Complete beginners will benefit from having every quantity explicit, while more advanced readers will be irritated and slowed down by the clutter. I can only suggest some rules of thumb:
Use both macrons and breves. Mark the vowel lengths that might be surprising, whether short or long. The lack of a macron is not a sufficiently strong signal of a short vowel.
Mark all vowels when introducing a new word. The reader can pick it up and supply the correct details later without repetition of the instruction.
Mark the length if a misinterpretation would be likely or harmful.
For an example of the latter, one of two elderly latinist friends of mine was a baron and the other one would sometimes address him as baro in Latin. He always marked the first vowel short to emphasize that it's the medieval word for a baron rather than the classical word for an idiot. Misinterpretation was unlikely as the baron's Latin was very strong but arguably there was a point in clarification.
When you mark a vowel, make sure you get it right. There's a separate question about that and you didn't ask about it, so I won't go deeper into it.
It is a matter of taste, but I would strongly suggest using the macron and the breve, not other diacritics for quantity. These two are universally recognised among your readers and unambiguous.
You can use the diaeresis to indicate that two vowels that seem to form a diphthong are in different syllables. This is how the distinction between aeris referring to bronze or air is often made.
