How should I categorize it? Morpholoically or semantically?

[Turama]

So I have two moods, imperative and desiderative (and much more). The desiderative however, can also work as an imperative. suatukhpitai literally means 'you're wanting to give it back to me' or it can also mean 'give it back to me', but with a more firm tone.

However where should I write about it? In the Imperative or in the Desiderative section? Or to generalize it, should I categorize morphologically (by morphology) or semantically (by meaning)? Which is more frequently used by 'professional' linguists or which is more suggested?

[mèþru]

I would put how each case is used within Morphology.

[Curlyjimsam]

I'd describe the functions of the desiderative in full in the desiderative section, but include a brief line in the imperative section to the effect of "The desiderative can also be used with imperative function: see section N".

A sensible layout would be to have the sections on both moods next to each other anyway, so it doesn't make that much difference! It may even (depending how much you have to say) be reasonable to have both within a single section under the heading "Imperatives and desideratives" or whatever.

[vec]

In highly synthetic languages, I tend to separate out morphology and syntax and put all usage rules in syntax, but in highly analytical ones, I combine the two under morphosyntax. If your language has multiple moods, you may want to roughly divide them by semantics before going into specific moods. Moods generically are either realis or irrealis, and either deontic or epistemic. Those super-categories may or may not be helpful in describing your language—the answer will really depend on the overall morphological structure and which other moods are present.