Let's break it down :)
"Make sure you read through the proposal and come". This should be clear enough for you :) [ Means you need to read the proposal and then come to the place, maybe office or discussion table]
"Be prepared to discuss it in detail ". this is also clear I suppose. [Means that you have to be prepared to discuss it in detail, this is like a warning/command/order. It is the subjunctive command form. (http://en.wikipedia.org/wiki/English_subjunctive) ]
When you combine these two, you get
"Make sure you read through the proposal and come prepared to discuss it in detail."
This is in subjunctive form and expresses an order/strong request/command for the person to READ the proposal, then COME and to BE PREPARED to discuss it in detail when he/she comes.