The effect of ionic surfactants and manufacturing methods on the separation and distribution of multi-wall carbon nanotubes (CNTs) in a silicone matrix are investigated. The CNTs are dispersed in an aqueous solution of the anionic surfactant dodecylbenzene sulfonic acid (DBSA), the cationic surfactant cetyltrimethylammonium bromide (CTAB), and in a DBSA/CTAB surfactant mixture. Four types of CNT-based composites of various concentrations from 0 to 6 vol.% are prepared by simple mechanical mixing and sonication. The morphology, electrical and thermal conductivity of the CNT-based composites are analyzed. The incorporation of both neat and modified CNTs leads to an increase in electrical and thermal conductivity. The dependence of DC conductivity versus CNT concentration shows percolation behaviour with a percolation threshold of about 2 vol.% in composites with neat CNT. The modification of CNTs by DBSA increases the percolation threshold to 4 vol.% due to the isolation/separation of individual CNTs. This, in turn, results in a significant decrease in the complex permittivity of CNT–DBSA-based composites. In contrast to the percolation behaviour of DC conductivity, the concentration dependence of thermal conductivity exhibits a linear dependence, the thermal conductivity of composites with modified CNTs being lower than that of composites with neat CNTs. All these results provide evidence that the modification of CNTs by DBSA followed by sonication allows one to produce composites with high homogeneity.