What if you want to change it's eye or eyelid colour.. but the .pet file doesn't HAVE a paintballz section?  where do you change it?  Okay...  

That's trickier and requires that you understand what you're looking at inside the file. With complex stuff I copy the .lnz out into a new file in the hex editor, save it as petlnz.txt, and open it in Wordpad -- not Notepad this time, Wordpad. Then I can see it laid out properly and see which number is which, changing numbers carefully. Say you have a pet with 244 eyelid and you want to change to 62: 

We start of course by removing the 4 from the end of 244, and increasing the 4 to 6, shifting it to in front of the 2, so that we just have an adjustment of 2 to make to an existing number as well as adding that extra 4 in somewhere: 

[256 Eyelid Color] 
244 -1 

changed to 

[256 Eyelid Color] 
62 -1 

Now, in linez, near the bottom we have: 

45 46 9 -1 244 244 100 100 0 0 
46 47 9 -1 244 244 100 100 0 0 
47 48 9 -1 244 244 100 100 0 0 
3 2 5 -1 244 244 95 95 0 0 
6 2 5 -1 244 244 95 95 0 0 

From the breedfile we see that in Linez the number columns are as follows: 
startball, endball, fuzz, colour, Lfcolour, Rtcolour, sThick, eThick, and then in the petfile there are two extra columns which usually contain zeroes and which it's wise to leave alone. 

Right! A couple of outlines are only 95 thick, so we can add a 4 onto one of those and reduce a 5 by 2, so as to get this: 

6 2 5 -1 244 244 95 934 0 0 

which would fix the size and the checksum. All okay as far as it goes, but that would produce a dreadful thick line which would "draw" on the screen at certain times when the pet moves (remember we've changed the thickness of the linez side) 

so you want to cut that down and spread it out a bit amongst the other outlines. I'd do that by changing the lines thus: 

45 46 9 -1 244 244 100 104 0 0 
46 47 9 -1 244 244 100 104 0 0 
47 48 9 -1 244 244 100 103 0 0 
3 2 5 -1 244 244 95 95 0 0 
6 2 5 -1 244 244 95 104 0 0 

See? Spreading the load, as it were, by reducing the 934 to 104 and increasing three 100s ti 104, 104, and 103. It's not as simple as when you've got paint Ballz to fool around with, but so long as you bear in mind what exactly it is that you're making larger or smaller, it all works out okay. 

When you don't have [Paint Ballz], it really depends on the individual pet as to what exactly you can change without it looking wrong. But I hope that helped