…that is the question.
English isn’t quite as fond of togetherstuck wordpairs as some languages, but it still comes close to loving them not wisely, but too well. Creating new words by compounding old ones is one of the main ways English expands its vocabulary (the other being outright piracy.) What this means for the writer is that at any given moment there are a number of English terms sitting uneasily on the hyphenated/unhyphenated fence.
The usual progression, in modern written English, goes from two separate words to a pair of hyphenated words to a single word:
hand held becomes hand-held becomes handheld
stand alone becomes stand-alone becomes standalone
hand book becomes hand-book becomes handbook
Handbook is a fascinating case. It started out in Old English as handboc, translating the Latin (liber) manualis — a book of a size to be held in the hand (as opposed to a honking great codex.) The word was replaced in Middle English by its snootier French equivalent, the Latin-derived manual, and manual remained the word of choice until the early 1800s, when hand book (or hand-book or handbook) was reintroduced by word lovers who wanted to return English to the purity of its Anglo-Saxon roots. The move was opposed, of course, by other word lovers, who regarded handbook as an ugly and unnecessary upstart, but the new (old) word caught on anyhow, and now we have handbook and manual both in our vocabulary as terms for more or less the same thing.
(A slight shade of difference does remain, however. Consider: given a Handbook of Emergency Procedures and a Manual of Emergency Procedures, which of the two books is more likely to fit into the pocket of a pair of cargo pants?)
So which spelling should you, as a writer, use? For those terms where there is a settled version, go with that one unless you have a firmly held preference for doing it the other way and are prepared to defend it. For the terms where the hyphenation issue is still in flux, pick the one you prefer and be consistent with it. Otherwise your longsuffering (long-suffering?) copyeditor† will end up counting all your uses of standalone versus stand-alone in order to figure out which one you’ve used the most — and cursing your name all the way.
†Another example of the hyphenization process in compound words. Most spell-checkers (spellcheckers?) will give a choice of copy editor or copy-editor, but all the practitioners of that trade whom I’ve had the good fortune to know have spelled it copyeditor.