Searching for Business Objects an Documents using TREX

Dear Experts,

I am new to TREX und have a requirement to index the SAP eShop (business objects) as well as several content repositories (html, pdf doc). I am pretty sure that TREX can index all these documents and objects. It is possible to search in these documents using just one search query? As I know, searching for business objects can be done only by using Ses / Embedded Search and the system ID has to be provided.Do I have to split up the search query in two further queries: the first one for searching in content repository (pdf, html) and the second one for searching in eShop (Business Objects)?

thanks for your help

Nicolai