Rather than - shows preference. This expression is generally used in 'parallel' structures. e.g - with two nouns, adjectives, adverbs, infinitives or -ing forms. e.g 1). We ought to invest in machinery rather than buildings. 2). I prefer starting early rather than leaving things to the last minute. When the main clause has a to - infinitive, rather than is usually followed by an infinitive without to or -ing form. e.g - I decided to write rather than phone/phoning. Instead of - suggests that one person, thing or action replaces another. Instead is not used alone as a preposition; we use the two words instead of. Instead of is not usually followed by an infinitive. e.g 1). I'll have tea instead of coffee, please. 2). I stayed in bed all day instead of going to work. 3). John was invited to the reception, but he was ill, so Jimmy went instead of him. Note - Instead (without of) is an adverb. It begins or ends a clause usually. e.g - She didn't go to Greece after all. Instead , she went to America.

If you are asking for the difference between the two in conversational English, there is no difference and they are interchangeable.