[poshbyro]

Can any one assist me on understanding chair conformations a little more in terms of the equatorial and axial substituents? I understand the fundamentals as in axial is obviously vertical and equatorial being horizontal. However I am having a hard time grasping the concept of the arrangement and determining whether or not a specific conformation is cis or trans.

I previously thought that any axial substituent pair were considered to be cis regardless of their arrangement on the chair. (1,2...1,3...1,4). With all that being said, any help on my understanding of this is greatly appreciated.

[Babcock_Hall]

I don't know what you mean by "axial substituent pair," but it does not sound correct.  Two substituents are cis when both point up or both point down.  One has also to keep in mind that equatorial substituents point either slightly up or slightly down.

[pgk]

You can make a paper hexagone and fold it to a chair conformation. With little imagination, this will help you to understand which pair of axial substituents corresponds to a cis- or trans-(geometrical) conformation.
But if it if still not comprehensible, you can imitate axial substitution with e.g. pencils, matches, toothpicks, plastic straws, etc. that are perpendicularly fixed on the edges of the hexagonal paper-sheet.
Also, this will help you to observe that axial/equatorial substituents pair correlation with cis- or trans- geometrical conformation, is not identical for each of 1,2, 1,3, 1,4, 1,5 and 1,6 substituents pair.