Have your tried using A4/A5 instead of SDA and SCL? A software change is necessary to enable the other I2C port.
For the other questions, there’s a lot of information in the Edison Expansion Board hardware Guide, there you’ll find the arrangement of the pins and the available configurations for each one, there’s also a multiplexing guide which you can also find in here http://www.emutexlabs.com/project/215-intel-edison-gpio-pin-multiplexing-guide. This includes the pull up resistors for the pins which are also configurable.
This has to be done from the Linux side, but there are examples that will teach how to do it.