How to use the phrase “if you will”?

Yes, this is a perfectly normal construction. The OED says in a note against sense 17 of the verb that:

if you will is sometimes used parenthetically to qualify a word or phrase: = ‘if you wish it to be so called’, ‘if you choose or prefer to call it so’.

So these all mean the same thing:

• To be honest, she wasn’t much to look at — a plain Jane, if you will.
• To be honest, she wasn’t much to look at — a plain Jane, as they say.
• To be honest, she wasn’t much to look at — a plain Jane, as the saying goes.
• To be honest, she wasn’t much to look at — a plain Jane, so to speak.
• To be honest, she wasn’t much to look at — a plain Jane, as it were.

You could also use a semicolon there instead of an em dash. But you really shouldn’t use a comma.

Also, you should understand that this is the deontic sense of will. That means it’s related to permission, obligation, and so on. It has nothing whatsoever to do with futurity, and it is not a marker for that here. It’s like “if you will allow”, but you don’t need to allow because will already means that.