Don't worry about, you'll get used to it soon enough. Generally speaking only the bit that modifies or is needed to distinguish it from other related words is written in hiragana. For example: 上がる and 上げる. Here が／げ is not part of the kanji stem, because you need to tell the difference between them and also 上る（のぼる）. Someone else can probably explain the historic reasons much better than I can.

Regarding 泊まる, there is a pattern of intransitive/transitive pairs (like 上がる／上げる above)   that are distinguished by あ／え so that bit is usually part of the okurigana for reasons of dis-ambiguity.
泊まる　泊める
暖まる　暖める
下がる　下げる
etc.