1. This isn't just an issue for CUs. It's an issue for churches. Of course, churches are practically limited in how broad they can be (they have to have a particular baptismal practice, for example, and you either have women preaching or you don't), but still, if you never have to work out how to get on with someone in your church when you disagree over doctrine it is probably because your church is too narrow.
2. The church is constituted by an act of divine sovereignty, by which the Father unites his Son to us, through the incarnation, and us to his Son through the work of the Spirit. Because it is an act of divine sovereignty, it is a given, not something to be achieved. When I come face to face with someone who disagrees with me within the church, I need to remember this fact. The church is not a club - not a free organisation of human beings, which I can be part of or not, and which I can casually exclude other people from. It is a creation of God.
3. The way we deal with secondary issues should reflect the fact that these secondary matters are really further definitions of primary issues. This throws up difficulties - for example, the Presbyterian and I both say that people are saved by grace through faith (primary truth!), but I can't see how his secondary idea of infant baptism can fail to contradict this, and he can't see how my idea of adult baptism can possibly be in line with it. Our ideas about baptism are a further definition of what we mean when we say 'saved by grace through faith'. So, the way I approach this difference cannot be to just live and let live - we have to both seek to give an account of our faith, explaining why our view on the secondary flows from the gospel. And as we do that, we have to keep reminding ourselves - keep believing - that the person we're talking does believe that same gospel, even if we cannot see it at the moment.
4. Jesus still rules his church. A discussion of secondary issues is not a comparison of opinions. It is a question of whether we will submit to the sovereignty of Christ over the church. Concretely, that means whether we will submit to Scripture, through which Christ rules. Therefore, the form of our disagreement must be exegesis and nothing else. As soon as something else comes into view - 'that opinion is old fashioned', 'that won't help our witness' - we are in the realm of our own thoughts and in rebellion against Christ. We start with Scripture, and end with Scripture. Only in so far as we are bound to the words of Scripture are we bound to the Word of God.
5. Where exegesis is the form of the disagreement, and where both sides are seeking to bind themselves to Scripture, we hope for resolution of the disagreement and we do not give up listening to Scripture together. In the meantime, we proceed by faith and work out how in practice we can have visible communion that expresses the invisible communion that we do have by faith. (It's at this point that Bish's posts come into play).