There are many questions here so I will stick to answering the one about the multinomial coefficient
$$\binom{N}{n_1,n_2,\cdots,n_m}\equiv\frac{N!}{n_1!n_2!\cdots n_m!},\quad N=n_1+n_2+\cdots+n_m.$$ This quantity may be interpretted as the number of unique ways of arranging $N$ items into $m$ categories with $n_i$ items in the $i$th category. For example, we may have $N=6$ balls with $m=3$ different colours and want to know the number of ways of arranging $n_1=1$ orange balls, $n_2=3$ blue balls, and $n_3=2$ purple balls; the answer is $6!/(1!3!2!)=60$ unique arrangements.
This can be derived directly from the knowledge that the binomial coefficient tells us how many ways there are of arranging $N$ into one category with $n_1$ items and another category with $n_2=N-n_1$ items, $\binom{N}{n_1}=\frac{N!}{n_1!(N-n_1)!}=\binom{N}{n_1,n_2}$. Then, one may realize that there is actually another category with which we want to subdivide our $n_2$ items, say into $n_2^*$ items with one label and $n_3\equiv n_2-n_2^*$ with another, and regular binomial coefficients tell us that there are $\binom{n_2}{n_2^*}=n_2!/(n_2^*! n_3!)$ ways of doing that, so the total number of possibilities is now
$$\binom{N}{n_1}\times\binom{n_2}{n_2^*}=\frac{N!}{n_1! n_2!}\times\frac{n_2!}{n_2^*!n_3!}=\frac{N!}{n_1!n_2^*!n_3!}=\binom{N}{n_1,n_2^*,n_3}.$$ Continuing and subdividing $n_3$ into two categories, by induction, we find that the regular binomial coefficients lead us to this definition and interpretation of multinomial coefficients as above.
So in the case of finding the number of microstates, we want to know the number of unique methods in which the particles can be arranged. Consider that we have $n_1$ particles of type $1$, $n_2$ particles of type $2$, all the up until $n_m$ particles of type $m$. Then the number of unique ways in which they can be arranged is $\binom{N=n_1+n_2+\cdots +n_m}{n_1,n_2,\cdots,n_M}$, which tells you the number of microstates.