Let's make it simple and clear:
Whether - use this word for indicating 2 options
If - use this word to establish a condition for an action.
Informally, "if" is sometimes used when "whether" is the better word, and in many cases this doesn't lead to confusion. This means that, informally, "if" is used in more than one way. However, "whether" only has one meaning, so using "whether" when indicating options is preferred.
1: How to determine whether my saddle is too high. (as in whether the saddle is too high or not--two options)
2: We should check whether everything is okay now. (as in whether everything is okay or not--two options)
Note: In both examples, the 2nd part of the expression "whether...or not" is implied. This is quite common and quite acceptable when doing so doesn't reduce clarity. This leads us to the next point.
You can correctly say "Whether you decide to come or not, give me a call." The shortened form, with the implied part 2, is "Whether you decide to come, give me a call." (I wouldn't write this because it reduces clarity. I would use the complete expression.)
One last comment: "Whether" doesn't need to be followed by a stated or implied "or not." The 2nd option could be any thing, as in "I don't know whether to buy cake or pickles."