You can see the difference in the codecs list on the main input tab.
Dolby TrueHD will be stated as TrueHD.
Dolby AC-3 will be stated as AC-3/E-AC-3.
FYI there's a difference between a TrueHD track as you'll find them on BD movie-discs, and one in a mkv container.
On a bluray moviedisc the TrueHD track also carries an independent AC3 track for legacy equipment. Eventhough this AC3 track is often referred to as the AC3 core, this is not the case. Both tracks are independent. Since BD movies are authored differently than mkv, both streams can exist within one "audio-track", so to say.
To be more complete, and for getting a better understanding of the word "core", DTS-HD MA is different in it's build-up. Such a stream really carries a dts core (such you'll find on a movie dvd) for - again - legacy reasons. Next to that core there is additional, dependent audio-data. Now these two combined will give the DTS-MA audio.
Within a mkv container it is not possible to mux both the TrueHD stream and the AC-3 stream as one track. You can, of course, mux the legacy AC3 audio as an extra audio-track with mkvtoolnix.
DTS-MA can be muxed as one track within mkv.
Should you encounter a file with only a TrueHD stream (which you cannot playback), you can convert this audio yourself with eac3to. It's a bit of a learning curve, but it's capable of decompressing the TrueHD track to the given number of channels in uncompressed PCM --> if need be downmix it to 5.1 with the proper settings --> and compress it to a legacy 5.1 AC-3 stream which you can directly import in mkvtoolnix.
A lot of people will have no sound during TrueHD/mkv playback and wonder why there is sound when playing the BD (or ISO) with "the same audio"? When playing the BD itself, often players auto-pick the embedded AC-3 track, which can be processed by the tv/amp/etc.
Hope this helps.