You don't just "organise your pens", though. It doesn't really work that way. Konmari says that you must first discard before you can store. So the very first category you do is clothing, subcategory "tops". You first empty out your tops drawer, your wardrobe, that chair in your bedroom, your laundry basket and any common piles or hooks. Pile them all up. Then go around every single room and double check there aren't any stray tops hanging around. Look on the backs of chairs, in other people's drawers/wardrobes, stuffed down the back of the bed or sofa, in a suitcase, left on the stairs, in a bag, etc etc. Any that you don't find in this sweep of the house, you are supposed to discard immediately when you find them later (because if you didn't miss them, they didn't spark joy). The only exception is clothes which are literally inaccessible - e.g. lent to a friend, in the wash, in a box in the attic etc. (Although if you had lots of clothes in storage I'd dig them out and do them all together rather than as two batches).
When you've finished discarding your tops, you can fold them as she says and place them back into a drawer, but it doesn't really matter where you place them at the moment - you've sorted them and tops are done and it doesn't really make a difference if they get scattered around any more (but hopefully, now you like all of them, you'll want to take better care of them anyway.)
Clothing is different really in that people normally have specific clothing storage, so once you've done ALL of the clothes, you could then do the "storage" part where you store by category within the clothes storage that you have. But the idea is that you discard in all categories and then don't worry too much about storing them again, until you've finished all of the discarding. Think about it - you reduce the entire content of your house down to what it needs to be, and then you can look at storage as a whole rather than doing it bit by bit.
So by the time you get to pens, you've kondoed a lot of things. There won't be that many places that pens can be hiding. But on the day that you decide to do pens, you go all around the house and search in every nook and cranny for pens to bring all of the pens together. Keep the pens which are nice to use or nice to look at (sparking joy!) and throw away the non working ones, the free ones, the broken ones.
When you've finished discarding you go back to storage from the first category again to the last. With something like pens you'll have ended up with a fairly small amount, probably, so by collecting them together again, even if they have strayed, it jogs your memory as to which ones you chose to keep. You'll know if you left the other one somewhere and if you did, you'll have a rough idea where it is. If not, it doesn't matter. Store them all together and when the other one turns up, put it away in that place too.
I didn't really understand this as much until I read all of the book - I only read the clothing part to begin with and did it as I went along. I think that's a good idea but definitely when you've finished clothes, read the parts about storage and why "tidying is magic" and you'll understand the method much better.