'The visible church, in the idea of the Scottish theologians, is catholic. You have not an indefinite number of Parochial, or Congregational, or National churches, constituting, as it were, so many ecclesiastical individualities, but one great spiritual republic, of which these various organizations form a part. The visible church is not a genus, so to speak, with so many species under it. It is thus you may think of the State, but the visible church is a totum integrale, it is an empire. The churches of the various nationalities constitute the provinces of this empire; and though they are so far independent of each other, yet they are so one, that membership in one is membership in all, and separation from one is separation from all . . . This conception of the church, of which, in at least some aspects, we have practically so much lost sight, had a firm hold of the Scottish theologians of the seventeenth century.' Dr. James Walker in The Theology of Theologians of Scotland. (Edinburgh: Rpt. Knox Press, 1982) Lecture iv. pp.95-6.
It should be clear that Durham shared the view of all the Second Reformation divines who 'had such a conception of the importance of the unity of the church, and such a horror of the evil of schism, and were so firmly convinced that anyone who withdrew from church communion without absolute cause, that is without feeling assured that he could not remain in such fellowship without committing sin, was guilty of a most heinous offence, that they were ready to give their most favorable consideration to any sort of suggestion of reasons why they should refuse to go out of a church, notwithstanding the existence in it of many corruptions against which they must protest.'
http://www.naphtali.com/articles/schism-separatism/the-sin-of-schism/
Song 6 Verse 2. My Beloved is gone down into his garden, to the beds of spices, to feed in the gardens, and to gather lilies.
He is 'gone down to his garden,' which implieth the similitude, formerly expressed, of a man's retiring from his chamber or closet to his garden: this 'garden' signifies the church, as chap. 4:12,15, and here, as opposed to gardens, in the words following, it holdeth forth the catholic visible church, as gardens signify particular societies, or congregations: the church is like a garden that is within one precinct, yet divided into divers quarters and inclosures: this being the church that hath the promise of Christ's presence, and where he is ever to be found, must be understood of no particular church, of which that cannot be asserted, that Christ shall be always there: it must therefore be the catholic church, distinguished from particular churches, or gardens.
2. He is gone 'to the beds of spices:' as gardens have distinct plots of flowers, and beds of spices, and some particular parts are allotted for these, where especially they grow; so in the church Christ hath his plants, whereof some are sanctified with grace (therefore compared to spices) and these, in some parts of the visible church, are more abounding than in other parts, (as spices in beds together, that may be elsewhere but in particular stalks and not so frequent) and as men love and frequent that plot of their garden most; so doth Christ most manifest himself in his ordinances ordinarily, where he hath his spices and lilies in greatest abundance: and thus this last part qualifies the former, he is in his church, but especially where his spices are most abounding: and therefore would you have him? Seek him in his church and amongst his people, and especially in such societies of his people, where true and lively believers are most to be found.
Here observe (besides what was observed on chap. 4:12,) Christ's church, tho' it have many subdivisions, yet is it one church; one whole catholic church, whereof particular churches are parts, 1 Cor. 12:28.
2. It is in that church and no where else, that Christ's presence is to be found, and where believers, the spices and lilies are planted.
3. There may be, in that one visible church, many more real converts in one part thereof, than in another; 'spices' in 'beds' are not in every place of the 'garden.'
4. Tho' Christ hath a singular care of, and respect for, his whole church, and hath a peculiar presence there wherever there is any part thereof, yet where he hath much people, beyond what he hath in other places (as in Antioch, Acts 11:21, in Corinth, Acts 18:10, and Ephesus, Acts 19:20,) there especially is he present, and there ordinarily continues he the power and life of his ordinances.
5. Those who desire Christ, should not run out of the church to seek him, or expect any way of finding him, which others have not found out before them but should seek after him by the ordinary means, in his church; for, this answers their question, 'Where is he?' proposed for that end, that they might seek him and find him.
Song 6 verse 9. My dove, my undefiled is but one.
She is one, which sets her out not only with unity in her affections, but (to say so) with a kind of oneness in herself: thus the visible catholic church is one garden, verse 2, comprehending many beds of spices; one church, made up here of many particular churches: and thus, oneness or unity is a great commendation to her, or a special part of her excellency.