My temple Guard with eternal Starhost and when near a hero will be getting +2 to save rolls as well as getting rerolls from my skink priest. But what happens if I roll 5 dice and I roll all 2's for my save? Can I choose not to reroll it and just add my modifiers or do I have to reroll it and risk rolling a 1 which would damage me?
In this case, you do not have to re-roll. If you read the celestial rites on the priest's warscroll it says you CAN re-roll run, charge, and save rolls. The can is the keyword.
I think rerolls are only made, if you fail? Ffor example if it's reroll 1s or "natural 1s" for example... so in the first case buffs and nerfs are added before you decide on rerolls, and in the second case you reroll before adding bonuses and malluses... Or am I wrong?
Not entirely true, there are some abilities where you must reroll, though most will say can or may choose instead of just reroll.
Usually, if you have a reroll, it states you may reroll, you can reroll, or a failed ---- can be rerolled. So usually it's a choice, and usually only takes effect if something is failed. Very few and far between are successful rolls required to reroll.