1. The Janet docs suggest `cond` as a replacement for if-if-else-else chains in other languages and `case` for `switch`-`case` blocks. That's a pretty good rule, although maybe you've already encountered that explanation? My main rule of thumb is that if the important value is "enum-y", representing a particular kind of thing or state, try `case`. If not, use `cond`. Neither Janet nor Clojure have enums (although you might be able to hack them in through macros or interop), so keywords usually serve that role.
2. I would prefer `when` to `if` because it's usually clearer what's going on. I usually don't use `and` in place of `if`. The trivial negation problem is an issue in basically any programming language that has `and`, `or`, and `not`, but it does add more options. Whether to use `and` or the equivalent `or`, I think your first instinct is often best.
3. I tend to favor threading macros (`->` and `->>`) when something is three or more functions nested and manually nested expressions for the rest.
For a total beginner, I would actually suggest forgetting about the more specialized options until you're comfortable. In other words, just use `cond`, `if`, and manual nesting. (Obviously still use `and` within the branches of `cond` or `if`.)