if the cylinders are concentric (I.D. and O.D.) ideally you would want to use FIM (full indicator movement, formerly known as Total Indicated Runout or TIR. the symbol is two arrows connected together). this controls the surface of one cylinder to the other over the entire length. paralellism would only do so in one plane, FIM does so in all directions. Simply define one of the cylinders, preferably the one that is the most important to the assembly, as the the datum, and define the other as: !fim symbol!.XXX!datum! where .XXX is the maximum runout allowed, and the datum is the specific datum to be referenced.
If the two bores are beside each other and are perfendicular to a face (such as cylinder bores in an engine block which are perpendicular to the mounting face for the cylinder head) then you would define the face as the primary datum. and preferably define two more planes mutually perpendicular to the face as secondary and tertiary datums so that you can properly define the location of the first bore. then define the second bore in reference to the perpendicular face (primary datum) and to the first bore which is defined as a fourth datum. This is how hole patterns are usually defined where the actual location of the pattern is not as critical as the pattern is to itself.
I would recommend a book entitled Geo-Metrics III by Lowell Foster and published by Addison-Wesley (ISBN #0-201-63342-6). Mr. Foster served on the ASME Y14.5M committee. And worked as a tooling designer at Honeywell for years. He also teaches courses in GD&T if your company wants to do that.