Once the Polybian reform marker is in your cities (you have seen the message from the advisor about changes to your military) you just have to increase the size of your factional barracks to get the new troops. If your click on your barracks you should see that it has a new bunch of troops to recruit and that none of the old troops will be available. As a side note when the Marian reforms happen your Polybian barracks will be destroyed by script and new equally advanced Marian barracks will be built in all your cities. You also get free level one barracks in all the cities that can recruit legionaries (there maybe an omission that I haven't noticed).