(Ultra) Luminous Infrared Galaxies ((U)LIRGs) are objects characterized by their extreme infrared (8-1000 $mu$m) luminosities ($L_{LIRG}>10^{11} $L$_odot$ and $L_{ULIRG}>10^{12}$ L$_odot$). The Herschel Comprehensive ULIRG Emission Survey (HerCULES; PI van der Werf) presents a representative flux-limited sample of 29 (U)LIRGs that spans the full luminosity range of these objects (10$^{11}leq L_odot geq10^{13}$). With the emph{Herschel Space Observatory}, we observe [CII] 157 $mu$m, [OI] 63 $mu$m, and [OI] 145 $mu$m line emission with PACS, CO J=4-3 through J=13-12, [CI] 370 $mu$m, and [CI] 609 $mu$m with SPIRE, and low-J CO transitions with ground-based telescopes. The CO ladders of the sample are separated into three classes based on their excitation level. In 13 of the galaxies, the [OI] 63 $mu$m emission line is self absorbed. Comparing the CO excitation to the IRAS 60/100 $mu$m ratio and to far infrared luminosity, we find that the CO excitation is more correlated to the far infrared colors. We present cooling budgets for the galaxies and find fine-structure line flux deficits in the [CII], [SiII], [OI], and [CI] lines in the objects with the highest far IR fluxes, but do not observe this for CO $4leq J_{upp}leq13$. In order to study the heating of the molecular gas, we present a combination of three diagnostic quantities to help determine the dominant heating source. Using the CO excitation, the CO J=1-0 linewidth, and the AGN contribution, we conclude that galaxies with large CO linewidths always have high-excitation CO ladders, and often low AGN contributions, suggesting that mechanical heating is important.