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I'm at the stage now where I've built a lovely mansion in the Falkreath Hold. I've furnished it and filled the barrels and cupboards etc., with loads of goodies for selling on or improving at a later stage.

I'm amassing a load of ingredients and it's high time installed an alchemy/arcane station.

Trouble is I have no idea where it will site, which means I don't know where to move my stash from or to given that if the new facility "replaces" an existing part of the build, you actually lose what you have in any containers or mannequins.

Can anyone advise?

I would have preferred the equipment and ingredient/potion storage to be housed in the cellar, which if I was designing the house would have made perfect sense. From what I have gleaned, I am led to understand that a complete new tower is provided.

Certainly when you have a prebuilt property as you have in Whiterun, Markarth, Solititude and Riften, the Jarls' stewards actually replace a children's bedroom with whatever you require, (I think!). Is this also the case with the "custom built" properties?

no , alchemy and enchanting stations have their own place in main hall and they won't replace anything there . you could also build alchemy tower and/or enchanting tower but their only use is to have dedicated space for for alchemy and enchanting , so they basically useless.
Only thing what will be replaced is small house interior when you remodel it to entryway so before you do it take all useful items from small house

Frodo-Baginses wrote: I would have preferred the equipment and ingredient/potion storage to be housed in the cellar, which if I was designing the house would have made perfect sense. From what I have gleaned, I am led to understand that a complete new tower is provided.

Certainly when you have a prebuilt property as you have in Whiterun, Markarth, Solititude and Riften, the Jarls' stewards actually replace a children's bedroom with whatever you require, (I think!). Is this also the case with the "custom built" properties?

The tower is a separate, new area of the house, and all your containers should be safe. It's located at the back of the house, accessed via a door near the cellar entrance (as illustrated).