I understand that both of these compounds are R but I do not understand why A is trans and C is cis.
In the case of cis-trans isomerism, you can refer to carbon molecules forming the carbon-carbon double bond as stereogenic centers. An example of cis-trans isomers is taken from here:
The carbon atoms that form the C=C double bond in 2-butene are called stereocenters or stereogenic atoms. A stereocenter is an atom for which the interchange of two groups converts one stereoisomer into another. The carbon atoms in the C=C double bond in 2-butene, for example, are stereocenters. Interchanging the CH3 and H substituents on the carbon atom on either side of the C=C double bond would convert cis-2-butene into trans-2-butene, and vice versa.