For some reason when I modify LevelUpSkillCount, LevelUpSkillPointsBase, LevelUpSkillCountPointsInterval and load up the game and type in advlevel my skill points per level are not changed. even if I set all 3 values to 0 nothing changes.

Same thing with any of the iXPLevel~ settings.. I still seem to get the same xp for everything I do.

what am I missing here?

I am definitely not a GECK expert so there may be better ways to do what you want, but here's my nebbish take on things for experience gains at least:

If you want less XP for killing enemies and for stuff like lockpicking, you need to change the iXPReward numbers, the lines that have the actual reward amounts...not the iXPLevel ones. Or alternatively, you could leave those alone and increase the numerical amount of XP actually needed to gain the next level by changing the iXPBumpBase from 150 to something else. 300 is a good starting point to try (early levels still come fairly rapidly but later ones can take longer). Or you can combine both things and really have slow leveling. http://geck.gamesas.com/index.php/Experience_Settings

As to skill points per level...if it's just for yourself that you're wanting that, so you can twink/test things or whatever your personal desire may be, my brief experimentation indicates it's often better/easier to mod one of those starter perks(?) (eg FourEyes) and then always pick it.

My problem is that from what I can tell, changing the correct values in game does not actually have an effect in game. So my question is if this is to be expected. That in order for me to change these values I need to use a script that changes them in game on load before they take effect.

I haven't tried using the console commands to quick-test changes, the things I mentioned work for changing the game for me...I only change the settings, I alter no scripting and XP gained etc. alters.

I do know that actually trying to directly alter only the player can be a little tricky. A lot of those settings are globals. Change the weightcapacity global setting, everyone can carry more, not just you. Hence why altering a Perk works better for some stuff, since it's applied directly to/your chr. But again, not an expert.