so stores like thimble and co, the philosiphers store and the stable smithy look as if they sell items that can be used to craft. i enjoy baking, but i cant figure out how to use yarn, layer cards and whatnot

Some of the items in thumble and co. actually aren't really used for anything. Some items there are requested for the nostalgic pet quest by Vanya, in the Arctic Frost, while others are more display and gallery type items. A guide to Vanya's quests is here: Vanya&;s Workshop Guide to Nostalgic Pets (UPDATED NOV 1)

The Philosopher's store items are used for alchemy combinations in the Alchove. A guide to alchemy is here; [topic not found]

The Sable Smithy items are used at Asmodeus Genetech Lab. And the combinations are variable. And you can find combinations for this at subetalodge.

Your pets can also fight with Sable Smithy weaponry that you create at Asmodeus Genetech. They kinda don't want to though. There are usually other better weapons for your pet's tier.

Hi , welcome to Subeta, and to the game of "I wanna make cool stuff"! There are three main ways of crafting: baking, genetech, and alchemy.

Baking is in Veta Lake: Fantines Bakery

You pick a recipe, and Fantine gives you a list of ingredients to bring, bought from Food Market.

Example: to make you can use +++++++++

This can get quite expensive. I tried it a while ago and decided that, although I love cooking IRL, in Subeta it isn't for me.

Genetech is in Darkside: Asmodeus Genetech Laboratory

You try adding two items together, or three items. They can be the same or different. 

Some examples: 
[item=unadorned steel sword] is made by combining 2 of the [item=iron ore] with a [item=stone sword mold] (items bought from Sable Smithy)

[item=used blue paint can] is made by combining [item=blue paint] with a [item=blue paintbrush] (items from Home Appliances)

[item=treasurefly] is made by combining [item=aeon] from Minion Market, [item=treasure map piece 4] from random events, and [item=black inkwell] from Thimble and Co.

A list of all known combinations is at the Subeta fansite SubetaLodge, as [user=nayo] mentioned.

There are also a few items which you can combine without going to the Genetech Laboratory! 

Example: if you have both [item=green Lovebird] and [item=blue Lovebird] in your Inventory, you can make [item=Pair of Lovebirds]

Alchemy is in Shadowglen: The Alchove

Items from Philosophers Store can be bought by anyone, but using them in Alchemy is only available to Zombies.

To be a Zombie, you need to have been through a Survival holiday to get bitten and infected, and develop a Zombie wardrobe Skin. That's mid February, so you just missed it: bad luck! D: If you enjoy Subeta enough to stick around long-term, then that's something to look forward to next year.

:) Hope this helps answer your questions, and please let me know if I haven't explained any of this well enough!