Yes, TotalPb is the sum of counts for 204Pb, 206Pb, 207Pb and 208Pb. However, you need to use a reference material with costant Pb concentration (a few of the zircon reference materials have variable U and Pb but constant U/Pb).
206Pb is radiogenic, but so are 207Pb (from 235U) and 208Pb (from 232Th). Concentrations usually refer to the total concentration of an element, and when you use one isotope of an element to calculate the total concentration, you assume that the reference material and unknown have similar isotopic composition. This is rarely the case for zircons, so using something like NIST610 to calculate a concentration might provide misleading Pb concentration values.
Regarding Input, Intermediate and Output channels: Input channels are those loaded from the raw data and are unchanged by iolite. This means that you can run the DRS as many times as you like and the input data will not be changed. Output channels are usually those that you would like to get a final value for (e.g. concentration channels, final U/Pb ratios). Intermediate channels are those used in the calculation process to get to the output values. An example of an intermediate channel is
Raw 206Pb/238U. It is unlikely that you want to report this raw ratio value for a sample, but it is part of the process used to calculate the final 206Pb/238U ratio.
I hope that helps. Please let me know if any of the above doesn't make sense. These are all good questions.