How can I tell who is who?
The best thing to do is ask, and be observant, whether or not you share a body with the person/s in question. If the being is unable to tell you their idenity or name, you should simply observe their mannerisms, voice, choice of words, posture, and so on, and use those as identifying traits so you know when you see the person again. This works from inside the body as well, although thought patterns and emotional states might be observable as well. For outside observers, there will often be sufficient facial expression changes and overt personality traits such that even the face may seem subtly or substantially different from individual to individual. Each person within a Multiple can be vastly different. Some are very adept at telling you their name and all about themself, while others are shy or unable to communicate for various reasons.
How can I tell who is thinking what?
In some systems this is very clear, while for others it can be very difficult. Sometimes one can tell by what the resident is thinking in general, because some people think about certain categories of things in specific or have a specific subvocal 'voice', but it's hard to tell some more generic thoughts apart, unless the person can identify themself. Some systems have little co-awareness, and have the exact opposite problem: they can't overhear each other at all.