It's one of those things where the more you do it, the easier it becomes. Since there's no time limit and resources respawn indefinitely you can pretty much just craft whatever over and over just to learn and get accustomed.
Core charges and using core items is just a fancy way of saying it's how you use items in an RPG. Once you create usable items like healing ointments, bombs, etc. you can place those items on your weapon. Go into the equip screen then press R. Unlike other RPG's, you actually create your healing item and depending on the recipe and materials used it can determine how good it is. The great thing is you can use the item indefinitely as long as you have a core charge. You start with 10, and you can see how much an item uses up by the bottom right circle on an item (CC - 1). So if you use a healing item 10 times, you exhaust the core charge, but you can use another item to recharge the core back to 10 mid-fight. To do this, hold Y for a few seconds and you'll see an on screen prompt. Once you use an item to recharge, it becomes unusable until you go back to your atelier or rest I believe.
Hopefully that helps explain it a bit.
