Yes you are right, for setting USB boot you muct put the jumper(Short the pins) of PMOD jumper (ie. J3). For detailed explaination of jumpers see AN75705 Getting Started with EZ-USB FX3 (http://www.cypress.com/file/139296/download).. Page 22.
Hope you have downloaded and installed the FX3 SDK(Software Development Kit) from Cypress site(http://www.cypress.com/documentation/software-and-drivers/ez-usb-fx3-software-development-kit). Follow the steps in the AN75705 Getting Started with EZ-USB FX3 to do that.
You can find the difference(if is USB boot or I2C boot) in the device list in the Control center Application. The device will be detected as 'FX3 boot loader device'.
If your FX3 board is a fresh new one then on booting with I2c mod you will find the device will be detected as 'Streamer Example device' and on pressing the reset button turns on blue LED(if connected to USB 2.0) or blinks blue LED when connected to USB 3.0.