Yes, book it in any staffed train station. There's no deadline, as long as the train doesn't fill up, and you have to have the pass activated at a station, any way. It's technically the Polish portion (from the border crossing point at Frankfurt Oder) which needs reservation, and those should be free to get in Poland, but the station agent will have to advise whether or not you can get that on the train. If not, German Rail might charge you up to €4.50.
At Berlin Hauptbahnhof:
Train Information and Tickets: The Deutsche Bahn Reisezentrum information center is up one level (OG1), between tracks 12 and 13, (open long hours daily). For those staying in western Berlin, the info center at the Zoologischer Garten station is just as good--and much less crowded.
EurAide is an English-speaking information desk with answers to your questions about train travel around Europe. It’s located at counter 12 inside the Reisezentrum on the first upper level (OG1). It’s American-run, so communication is simple. This is an especially good place to make fast-train and couchette reservations (generally open Mon-Fri 11:10-18:50, until 20:00 May-July and Sept, check website for specific hours, closed Jan-Feb and Sat-Sun year-round; www.euraide.com).