Will the EHT set in "WinTMCA" software be always applied to the PMT connected or will it be applied only during the counting time?
Unfortunately, it's impossible to provide information about the EHT set in WinTMCA, because it's nowhere to be found. You will have to consult the built-in Help file. The database should contain information related to the way the software works and the supported features. Go to Help > Help Topics to find more about this.
Additionally, download the PDF manual: http://www.qsl.net/k0ff/01%20Manuals/Software/ICX-Thermo/ICX-THERMO-winTMCA32%20software-manual-en.pdf