You need to set your integration (assuming single file) with header and line and group by something you have in the file at the header level (such as batch number) that is the same on all lines.
The sample Inventory Transaction integration in IM has header / line/ serial objects but is a good example on how to setup a group by as that groups by Document Number. I'd almost recommend splitting it up a bit though as that is quite alot of lines on a single transaction but I would assume it will work. I've certainly done north of 5000 lines on a cutover in a single IM transaction.
Thanks Tim - I appreciate your response. You helped me find the direction I needed. I took a deeper look at the IM example for Inventory and as you mentioned, I played with the header/detail files and got it working.