Importing Products to multiple categories

I have a customer with 30,000 mundane products that she's pulled of ZenCart in a very flat file. No variations, all pretty simple stuff with unique SKUs, small descriptions and names. It's actually quite a small file.

We need to import these either using a) the standard CSV importer b) using a third part CSV importer or c) a script that my developer will write to manage this. So far so good.

QUESTION: We need to attribute some products (about half; 15,000) to two categories. Any ideas how we can tackle this before we start the job?

PS - I assume MarketPress does handle 30,000+ products..?

Thanks in advance.