If you press CTRL / or CMD / it will put // at the beginning of the line and the comment will be properly indented.
// comment with two indents
For this to work Comment at first column must be checked in Editor->CodeStyle->Javascript->Wrapping and Braces->Keep when reformatting like mentioned in another answer.
This screenshot is for Java, but it works the same for Javascript. Just choose javascript in the menu
If you want to write multiline comment you can use CTRL SHIFT / or CMD SHIFT / That way when you go into new line, you will have one space after the comment start
/*
* there is space before this*/