Yes you can use multiple feed plugins for JobRoller available from the
AppThemes marketplace. The Indeed feed is built into the theme by default, whilst the LinkedIn Publisher, CareerJet and SimplyHired plugins are are marketplace items, but they are all designed by AppThemes so of course we do and are able to ensure they are able to work together.
In terms of search, I found some notes from one of our development team which perhaps explains how it works in the theme for feeds:
Our Indeed implementation always shows contextual results while keeping the results limited to the site owners job industry (defined using keywords on the job listing queries field). The only exception is for searching. In this case, the keywords set on the job listing queries are ignored in favor of the search keyword.
Thanks.