Here is how I've been doing it, I believe I am correct. I'll give a hypothetical example and explain as I go.
Joe Traveller decides he wishes to leave his homeworld at the ripe age of 18, and thus signs up with a free trader. (i.e. he takes one term of Merchant). After this term, although he gets promoted to 01 in the Merchants he doesn't get a cash bonus, and thus jumps ship at age 22, and decides that he can best serve the Imperium and get to see the stars by enlisting in the Navy. (Otherwise, he musters out of the Merchants, and joins the Navy at start of term 2) Joe likes Navy life better, and stays in for three terms, getting comissioned and promoted to a Navy rank of 03.
Okay, how does Joe muster out?
Well, first he does his 1 term as a merchant, where he's an 01. Since he spent a term as a merchant, and got promoted to 01, Joe gets two rolls. He can take them as two cash rolls, one cash, one material benefit, or two material. Joe decides to take them both as cash. Later, he spent three in the Navy, and made 03 in the Navy. Joe now has 5 rolls, 3 for the three Navy terms, two more for rank. Joe can take one more cash roll if he likes (one can only take 3 cash rolls, period, not counting cash bonuses), or he can take them all as material. Joe decides to use his last chance for a cash roll now, and four material.
To sum up, Joe has two rolls on the Merchant table, one for the one term, one for rank 01. He has five on the Navy table, three for the terms, two for rank of 03. As I understand it, it's best to muster out of each service before switching career paths. This might be manditory, this might not, but if you look, a lot of the material benefits are stat increases, which could affect skill points (bonus to Int), if a character can get into University easier (bonus to EDU) or if the character could now qualify for the Noble class, where he couldn't before (bonus to SOC).
Hope my rambling made sense, I must admit I'm functioning a slight lack of sleep, mild insomnia. Please, if I am wrong or if someone can sum up better then I can, feel free to post.