If their thermal conductivity can be lowered, polyacetylene (PA) and polyaniline(PANI) offer examples of electrically conducting polymers that can have potential use as thermoelectrics. Thermal transport in such polymers is primarily influenced by bonded interactions and chain orientations relative to the direction of heat transfer. We employ molecular dynamics simulations to investigate two mechanisms to control the phonon thermal transport in PANI and PA, namely, (1) mechanical strain and (2) polymer combinations. The molecular configurations of PA and PANI have a significant influence on their thermal transport characteristics. The axial thermal conductivity increases when a polymer is axially stretched but decreases under transverse tension. Since the strain dependence of the thermal conductivity is related to the phonon scattering among neighboring polymer chains, this behavior is examined through Herman's orientation factor that quantifies the degree of chain alignment in a given direction. The conductivity is enhanced as adjacent chains become more aligned along the direction of heat conduction but diminishes when they are orthogonally oriented to it. Physically combining these polymers reduces the thermal conductivity, which reaches a minimum value for a 2:3 PANI/PA chain ratio.