With the upgrades, you will need to balance both sides of the trees if you wish to beat the ending. You'll need to upgrade both the close range scythe attacks, as well as the long range cross attacks. At the end, you'll have to resort to one without the other, and then vise versa soon after. If one is left un-upgraded, you're going to have a very hard time beating the final boss in this game.
As you may well know, you will have the chance to upgrade the unholy tree in this game as you progress deeper into the storyline. This tree is strictly for damage dealing attacks, focused mainly around your scythe. At a certain point in the upgrades, granted you press the right buttons, it will make it near impossible for any enemy to get near you without getting sliced to bits. Upgrade this one if you feel safe dealing close range attacks.
As you progress through this game, you'll be given the option to upgrade the Holy Tree abilities. The important thing to remember is that this tree is less for fighting perks, and more for protection. This tree offers long range attacks, and abilities that will lower the amount of damage you take from attacks. At a certain point, it may completely make you invulnerable to attacks for a short period of time. Upgrade this tree if you feel safe attacking enemies from a distance with holy cross attacks.