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I was trying to get familiar with the rules and using this rules and a Ogre(link) I was increasing his CR to CR6, for this I look at the table of the link and I see I had to increase HP+40, AC+4, Attack roll +5 and damage +10, I keep the same size.
The things I dont get is..now is a CR 6 Ogre no? so I have to increase 1 point of his abilities and and 2 feats no?but iniative, BAB, CMB, CMD, for example the BAB never change no?

So I tried to search for some tool or web it makes all of this for me and that way see if I was doing it right, I found combat manager and I pick the same, and Ogre and I add 3HD to him but the program says is CR4 and it add BAB and dont add AC... http://i.imgur.com/4UQHXKQ.png

So I suppose the program is doing it right I dont understand how to increase CR of the monsters

Question 2:Is not better use always the advancement with class levels?even if it is more difficult

EDIT: When I look at the Table 1-1 the values are right and the program value are wrong.(The programs says 52HP for a CR4)