What does it mean to have a 1K QPS limit per user and 10K QPS 100 seconds limit ?
What is a "user" ?
If I have two remotes, using the same api, with 2 different sa accounts does each one has a limit of 1k ?
One regular "personal" account is one user.
A service-account is one user.
Thus if you have two service accounts they use separate quotas.
To be perfectly accurate here (and to answer your title directly) I will say that one Google project will generally have 10.000 queries-pr-100-seconds total, while a single user will have 1.000-queries-pr-100-seconds. In other words you can (by default) have 10 users going full blast on the same project without the need to request further quota from Google. (which should be plenty for any personal needs and then some).
However if you wanted to make a public app (like rclone, which has a default API key) it would not suffice, and you would need to request Google for more quota (which you'd probably only get if you can demonstrate you have a real need for it).
If by "API" you mean the Google Drive API, then yes.
Your two users are unrelated and have separate (private) quotas. (1000-queries-pr-100-seconds)
If you have two different systems that might do heavy heavy activity at the same time then having them as separate users (or service-accounts) may be beneficial.
That said, the standard quota of 1000 requests pr. 100 seconds is generally more than you need for most use-cases. It heavily depends on the spesific use-case of course, but most users need not really worry about the API limits as they will rarely exceed them except in short burst-activities (which rclone will handle/throttle automatically).
I hope that clarified what you were aiming to understand. If not - feel free to ask follow-up questions 
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