creating a table with item, origin, destination.
what is the best way to index the table when the user may
query by either item/origin or item/destination?
Do you mean 'Selecting the Primay Index' column?
There's a lot we would need to know to help you and to be accurate, but I would make your PI on Item, knowing almost nothing about your data. Give it a try, it can't hurt!
Create the Primary Index with a colum of more unique values.
While creating Secondary index you need to see -
1) how frequently the combination of columns are being used in retrival. if usage is more then only prefer SI.
2) if any utilities such as Fastload, multiload are being used then rethink of creating SI