The Punnett Square is a way to determine possible combinations of
alleles and expected proportion of genotypes from 2 parents Each
parent will contribute one allele for any trait, so there will be a total of
2 sets of 2 alleles each for each trait.

The first step is to separate each set into it's individual alleles, and
place each allele as the 'heading' of a window-pane kind of square.

In this example, one parent is Heterozygous Black (Bb) and the other
is homozygous chocolate (bb).
bb split to:

b                b

Bb

Bb

bb

bb

Bb is       B
split
to:  
   b
By matching the outer 'labels' and placing them in the
boxes, all possible combinations are determined.  The
expected outcome of progeny at the B locus would be
50%Bb (black) and 50%bb(chocolate).



This can be done for as many alleles as is known for the
parents, and we can do Punnett squares for more than
one gene at a time: In this example, if the parents entire
known genotypes were:

EeBbdd    a blue (The dd dilutes the EeBb black to blue)

and

eeBBDd  a yellow with a black nose.

You would need to make a 'heading' on the outside of the
box for every possible combination of each gene series.  
The possible combinations for the EeBbdd are
EBd,Ebd,eBd,ebd.  The possible combinations for eeBBDd
would be eBD,eBd, eBD, eBd.  When you are splitting up
the alleles you are basically assorting the genes into
packets as if they were gametes!
EBd                      eBd                     Ebd              ebd

EeBBDd

eeBBDd

EeBbDd

eeBbDd

EeBBdd

eeBBdd

EeBbdd

eeBbdd

EeBBDd

eeBBDd

EeBbDd

eeBbDd

EeBBdd

eeBBdd

EeBbdd

eeBbdd
e
B
D

e
B
d

e
B
D


e
B
d
Both EeBBDd and EeBbDd are black, so 1/4 are black.
Both eeBBDd and eeBbDd are yellow, so 1/4 are yellow.
Both eeBBdd and eeBbdd are diluted yellow (cream) so
1/4 are cream.
Both EeBbdd and EeBBdd are  diluted black (blue), so 1/4
are blue.
Real Life Example
A yellow F1 Labradoodle female with a black nose (eekkBBDD)
was bred to a blue poodle carrying yellow, and brindle
(EeKkbrBBdd).  The predicted phenotypes would be 50%
yellow, 25% black, and 25% brindle.  Below are the puppies
and the Punnett Square!
50% Yellow
25% Black
25% Brindle

EekbrkBBDd

EeKbrkBBDd


eekbrkBBDd

eeKkBBDd

EekbrkBBDd

EeKkbrBBDd


eekbrkBBDd

eeKkBBDd

EekbrkBBDd

EeKkbrBBDd


eekbrkBBDd

eeKkBBDd

EekbrkBBDd

EeKkbrBBDd


eekbrkBBDd

eeKkBBDd

ekBD

ekBD


eKBD

eKBD
EekbrkBBDd  are brindle (first column)   25%

EeKkbrBBDd are black   (second column)   25%

eekkbrBBDd   and eeKkBBDd are cream  (last 2 columns)   50%

EkbrBd         EKBd            ekbrBd       eKBd