Basically you use the weapon in battle until you see that it is maxed. You need 2 weapons that are at max in order to combine them. You can ask Toady to analyze a weapon to see which one it is best suited to fuse with.
Pretty much any combo will give you a stronger weapon, though some are better than others of course. It doesn't take long at all to max out a weapon either. It can be very useful in obtaining some strong gear.
Make sure to have Toady analyze first! If only for the sake of knowing which is the best weapon to fuse with!
In all honesty, this is my biggest complaint about the game. I knew you could use Toady as soon as you got him, but I didn't like the fact that they made him an item in your inventory. Not because it takes up space, but because they have the Frog Log that only shows the recipes, and doesn't offer the option of combining the items right then and there. It's stupid. -_-
Weapon combinations are simple in this game. Except for certain ones you need a specific type of. You don't need a guide to make best weapons for the characters, just keep combining weapons and you will eventually get them. Rarely it might tell you that the combination might not result in anything better, just max a different weapon out and combine with it instead. Toady will tell you if you are gonna get something bad, if not it will always be better than what you got. The guide does nothing but confuse people about weapon combining.
Don't listen to Toady either on his suggested combinations, don't go out of your way to do that, if you got 2 weapons maxed, feed them to toady, and if he says nothing, it will be better than the strongest weapon you fed him, simple as that. Sometimes you will get a better version of a certain weapon, which is still a better weapon.
It's still worth analyzing, though. You don't have to listen to his suggestions, but it's worth seeing them.
1: Toady's Suggestions will ALWAYS lead to a result that is better than both components. 2: Ignoring them will USUALLY do so, but MIGHT NOT (he will warn you if it will downgrade). 3: Jaster's unique swords CAN be upgraded with Toady, provided the weapon you combine them with is strong enough. (For example, combine the Desert Seeekr with a sword that has a level requirement in its teens, and you'll get the Desert Seeker II.)
Also, if you analyze at least 100 different weapons, and make 50 recommended fusions, you qualify as "complete" for the Frog Log entry on MIO's checklist.
"As the good archmage often admonishes me, I ought not to let my mind wander, as it's too small to go off by itself." -Danilo Thann
Making 50 weapons is entirely too much work, and these are 50 weapons that most you don't even need, when many of the ones I created normally, which were a ton of them didn't even count toward the 50, kinda stupid huh? And its not even rewarding if you do it. I'm not a completion freak in any game. Some people are and the ones that are I'm sure dread having to do this.