With certain words, like yojijukugo and most sino-Japanese compounds, you pretty much have to use kanji, and there are a lot of general conventions, such as not using kanji for auxiliary verbs. However, in many cases, it can be a question of the individual's stylistic preference. You'll notice different people write the same thing different ways, and even the same person might use a particular kanji in one sentence, and not in the next (even within the same paragraph).
I've heard people talk about getting a 'balance' between kanji and kana, so if your sentence is looking a bit squiggly, you might use some slightly less common written forms like 出来る. The best way, for now, is to use the first choice that the IME pops up (assuming it's the right homonym), since this is generally the most commonly used one. Outside of that, you'll pick up the conventions quite quickly through reading, and start to develop your own personal style. I've got to say though, I couldn't even read 為ます, and it's a good example about my IME point, since it's not even in there
The forms you mentioned for the ko-so-a-do words were used in some of the early 20th century stuff I tried reading (Souseki and Akutagawa), but there have been a lot of changes to the writing system since then.