As you have the 3206 MSO it can collect 128,000,000 samples into its internal memory. Firstly make sure the max buffer memory is set to more than this - say 200MS. Its the control 2nd on the right from the timebase.
Next to make sure you can use the full buffer use single shot trigger otherwise half the buffer will be used for the displayed waveform and half the one you are collecting.
The streaming mode mentioned uses the internal PC memory at slower sampling rates / long timebases but will not really make much difference as its limited to 100,000,000 samples. It will happen automatically at around 100ms/div although under tools / options / sampling you can adjust this.