I'm a bit confused on how to set up my store.
I have multiple products, like ink for printers. Manufacturer | Printertype (inkjet/laser/led) | Printer | Cartridge.
1 cartridge can fit into many printers and maybe (whitelabel) from different manufacturers.
Visitors can search on manufacturer, printer, or on cartridgenumber. Should I put these names (Canon/HP etc) in categories or attributes.
What gives the best workflow and search flow (for the visitor).
Really it depaned on how you want your site to work.
If when looking at a category list/grid you want customers to be able to fitler the products by Manufacturer / Printer Type, which might be useful. Then you should put them as attibutes and make those attibutes filterable.
To enable these to be searchable then create them as attibutes and make sure to allow the attribute to be searchable.
If you want to add them into the menu the easiest way to do this is create a category, say HP Printers.
There's no reason you can't have them as both category and attribute.
Personally I'd have Manufacturer, Printer Type and Cartridge Number as attributes. Manufacturer and Printer Type as filterable attributes and all 3 as searchable. In fact Manufacturer is alreay an attribute.
For Pinter (printer the cartridge will fit into) I'd have a filterable attribute, but set the attribute type as multi-select so you can select all the printers the cartridge fits into.