I am following Logan's mod list and I am at the point to install the texture pack combiner with all of its packs. I was wondering do I have to use the texture pack combiner for the texture packs that allow to download them with the nexus mod manager.
I'm not 100% sure I understand you question, but the texture pack combiner's functionality is not dependant on how you download or install the texture packs. Doesn't matter how you download any mod(manual or with NMM) as long you install with NMM, easier to keep track and to install.