The first equipment you find with enchantment slots will probably have them filled, but you'll start finding some with open slots, as well. Check out Derk's equipment offerings for the unique items I mentioned above the next time you're in the village, for what enchantment slots should look like.
Generally, you will eventually remove most enchantments and replace them with ones suited to your preferences or needs at the time. Most level 10 enchantments and all healing aura enchantments require a moderately rare malachite gem to enchant, so usually at the start of the game you should leave healing aura as they are, unless you don't need the equipment but want the enchantment formula (though since they all require malachite gems, you might want to ignore lower level formula and just wait until you can get level 10, or 9 if that takes awhile).
There are a couple malachite gems you can find or buy fairly early, though.
After you take over the battle tower you can re-enchant everything whenever you upgrade equipment with little to no effort. Before then enchantment ingredients will be limited, so you'll need to be a little more conservative. For example, if you find a new piece of armour with Life Line 4, and you have the formula for level 6, you might want to hold off until your next upgrade to use your limited ingredients, since level 4 to 6 isn't a huge difference, considering the next piece of armour you upgrade is probably not going to have Life Line at all.
That said, I didn't have too much trouble keeping Life Line on armour and Static Charge on jewellery, and only checked vendors for ingredients a couple times.
