Never used SharePoint before and have been given the task of setting up SharePoint Online and migrating list from SharePoint 2001. I set up subsites, however I now know that I cannot create lookups between subsites. So what is the best way to set this up. All my lists need to lookup each other and be viewed by different departments. I had created subsites for each department but now my lists down "talk" to each other. Should I just have no subsites and use pages for each department? Is so, can I easily move my lists to the parent site?

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Like you said look-up columns only work between lists the resides on the same (site)-level. So if you need the list to lookup between different apartment sites you really have no other option than to place all of it on the same level.

Aaaaaaand then theres a small workaround for specific use-cases that you might be able to use.

IF the list you want to look up is placed on the top level site, you can create a site column as a lookup to that list. Now this column you can use on subsites.

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