I think I know what you are referring to. A while ago, I was first into my Japanese classroom, at which point my Japanese teacher asked me something like 「ここに5分ぐらいいますか？」, to which I was perplexed and didn't have a ready answer. The main source of my confusion was the nature of Japanese 'present tense' expressions also having a 'future tense' aspect. I will expound on that somewhat.
いる generally means 'for an animal or human to be present (exist), in general or in a specific location'. This can be used to imply remaining in a place as well. In English we might say "Will you be here for 5 minutes?" rather than "Would you wait here for 5 minutes?". The same is true in Japanese. Below are equivalent examples of the corresponding English question in Japanese:
5分ぐらい（私を）待ってくれませんか？ ＝ 5分ぐらい（ここに）いてくれませんか？
While the above sentences are fairly equivalent in overall meaning, the main difference is that one is transitive (active) and the other is intransitive (inactive).
When using the word 待つ, this is an active process (waiting for X). Therefore the particles used must reflect this (ここで待つ / 私を待つ).
When using the word いる, this is an inactive process. You are simply 'being'. Therefore, the corresponding particles used would not be the same (ここにいる / 私がいる）. Although いる seems to be more readily translatable as 'stay', rather than 'be', this is a distinction that does not apply in Japanese. In this sense, 'stay' will also be intransitive.
The が and に are used for simple state of existence verbs like いる, while は and を are used for verbs where an action is being performed.
With more advanced sentence constructions the particles can be fungible (は vs. が, etc.). For your question, however, it would be helpful to have specific examples of sentences where you are unsure of why a particular particle is used rather than another.