If you are looking at this page then you and I agree the explanation on the previous page was clear as mud.

This page merely has some example sequences and what I found to be the programs output for these sequences, when it is working properly(I think.. see the disclaimer!).

To check that the program is working see that the program yields the following pI values:

For individual amino acids please realize that there is a range of pH where some of the following are essentially neutral.  Also, for instances where a sequence has only negative or only basic charges, the endpoint 0, or 14 will be reported.  The program does not currently report the pH at which an input sequence is not charged.

Aspartic Acid  D  =  4.05

Glutamic Acid  E  =  4.15

Cysteine  C  =  5.48

Tyrosine  Y  =  5.48

Lysine  K  =  8.71

Arginine  R  =  9.71

Histidine  H  =  6.7

Alanine  A  =  5.485

Try input  EE  =  3.869

Try input  EE, and select 'blocked' C-terminal, and specify '2' for number of N-terminal residues  =  6.022

AAARG  =  9.71

AAARG  with N-terminal 'blocked'  =  7.775

AAARG  with C-terminal 'blocked'  =  14.0

AAAEG  with N-terminal 'blocked'  =  0.0

EERRRG  =  9.471

EERLRG  where 'L' will be an Arginine you suspect has a specific pKa value of 12.7, and you have input 12.7 as the pKa in New Residue Slot #1, number of residues '1', and 'positive' residue  =  9.538

YARRRYG  =  10.903

YARRRpYG  where 'pY' signifies a phosphorylated Tyrosine(For illustration only.. do not input 'p' in the FASTA sequence), and you have noted this by doing the following:  You input YARRRYG for the sequence, input '2.0' for pKa modified Tyrosine(this is an example, I do not know the pKa of phosphate in Urea solutions), input '1' for number of modified residues, input '5.9' for pKa of New Residue Slot #1(again, just arbitrary pKa for example), input '1' for number of residues, and select 'negative'.  The selection of '1' for modified Tyrosine will nullify the Tyrosine present as an internal residue in the sequence, which will be replaced by the '1' modified Tyrosine with pKa '2.0'.  The output will say '0' Tyrosine at this point because both the internal Tyrosine has changed, and the N-terminal sidechain Tyrosine is going to be accounted for by N-terminal side pKa.  The pKa here, for this unmodified Tyrosine, will be the default value for Tyrosine.  The output of this input should be  = 8.71

pYARRRpYG  For this sequence input the following:  input YARRRYG for the sequence, input '2.0' for pKa of N-terminal side residue(remember note (9) from the previous page).  This pKa of '2.0' will be considered for a negative residue if 'Y' is present as the N-terminal residue.  Input '2.0' again for modified Tyrosine pKa, input '1' for # of modified Tyrosine residues(remember N-terminal side residue is taking into account the other modified Tyrosine residue).  Now the # of Tyrosines will be '0' in the output.  Input pKa of '5.9' for New Residue Slot #1, and input '2' for number of residues for the 2 secondary Tyrosinephosphates.  The output of the above input should be  =  5.88.

Again, I do not know how accurate this will be ex silico, or even if the prediction here is an accurate theoretical prediction for a phosphorylated residue in an amino acid sequence.  Depending on input values of pKa the program can be more accurate.  

To check the program against SwissProt(see previous page reference [1]), you should get the reference from Bjellqvist noted on the sequence submission page, to use the corresponding pKa values that SwissProt uses.  For example of this please see above that 'AAARG' will give a pI of 9.71, while entering 7.59 for the pKa of the N-terminal amine will give a pI of 9.795, quite similar to the pI computed by SwissProt.  Again, as noted on the previous page, this is due to an average value of pKa for N-terminal amine being used at nihilnovus.com, while at SwissProt the effect of N-terminal side chain on the pKa of the N-terminal amine is taken into account more accurately with regard to the Bjellqvist paper.