Thinking back on my previous post, a comment on Collste's introduction to applied ethics, I've decided my treatment suffers from the same problem I see in Collste's piece. The discussion is too short to clearly distinguish two different uses of reflective equillibrium, one where RE serves as a structure for argument, the other where it acts as justification. So let me try that again.
First, RE as a formal tool: If a suitable course of action has been picked out, or one that you believe is suitable, you can try to explain why by showing how that action sits in a reflective equillibrium. That would consist in stating the various relevant factors, drawing out the conflicts between them, staking out a suitable give-and-take between these factors and indicating how the chosen course of action fits appropriately between them. To say it in a different but equivalent matter: for relevant facor X, determine how the other relevant factors Y, Z, etc. impact on the demands of X to determine X', being the demands X makes in this case compared to Y, Z, etc, and do so for Y, Z, etc. as well; the appropriate course of action C is one which fits X',Y',Z' and so on. The fact that the appropriate course of action is so is explained by it respecting all the demands of the relevant factors as measured against the others.
Of course, not every candidate course of action can fit in such a reflective equillibrium. If it doesn't, you could try to use RE as a method to find the right course of action. Let us say the most attractive candidate course of action C meets demands X' and Y', but not Z or even an appropriately modified Z'. There could be a change to C to make a C' which might fit the bill, or if no such change is forthcoming, perhaps a further modification to the apparent demands of the various factors, maybe making a X'' which leads to changed demands on Y' which makes a Y'' and a Z'' which a C or C' could meet. Because you have made moves to change your approach to the case, and have done so based on RE, RE has done substantive work here. This is different from the former case, where RE does just formal work.
So, to sum up in conclusion: where the course of action one picks is picked independently of RE, and RE is used to explain why that is the right thing to do, there RE only does the formal work of structuring the argument; however, you might be tempted to change your approach based on what would bring about an RE, and that would be to use RE substantively, to choose to do this rather than that, and even (in what Rawls calls cases of 'wide reflective equillibrium') to modify your approach in other relevantly similar cases.