The UP Squared has been tested using Ubuntu 16.04.3 64 Bit Desktop and ubilinux 4.0.
To take advantage of the 40-pin header you can download the official distribution ubilinux 4.0 (Based on Debian Stretch).
Otherwise you can download the Ubuntu image from the official website:
To prepare the installer you can use your preferred software for creating Linux USB installer.
For Windows users we suggest to use the following tool: Rufus
Later in August, Yocto and Ubuntu specific Kernels with support for the 40-pin header will be available for download.