This is pretty easy. You need ca-certificates to be installed (but Debian doesn't guarantee those certificates are valid). So if you have this packages installed, copy your CA to /usr/share/ca-certificates/yourCA.crt (must have .crt extensions) and then run dpkg-reconfigure ca-certificates.
Debconf will show you the list of certificates in /usr/share/ca-certificates/ and let you select those you want to trust. Yours, of course, appears in the list.
That's all.