I would like upgrade spamassassin and clamav manually. I'm not sure how to do it. It seems to me that only replacing the old to the new version in /home/admispconfig/ispconfig/tools/ could do it. Right?
Yes, just replace the installations in the subdirectories of /home/admispconfig/ispconfig/tools/..... For the correct compile settings, have a look at the install_ispconfig/compile_aps/compile script in the ISPConfig installer tar.gz file.