My apologies for the late response. It's good to hear you've already come as far as you have. Some responses to your questions.
1. If you want to have your generated software run from boot up, there are some manual steps. You need to copy the generated application (<modelname>_interface) from the directory you generated in to the SD card (/mnt) on the hardware. You then need to modify init.sh to start your application rather than the default sdr_firmware.elf.
2. There is a two step process to changing the IP address. Firstly you need to change the IP address on the board, which can be done using the dev object:
>> dev = sdrdev('ZedBoard and FMCOMMS2/3/4');
>> setAddress(dev,'IPAddress',<new IP address>);
Next, you need to change the zynq() object IP address also. It tells Simulink which address to communicate with the device when deploying or running External Mode.
3. Assuming you mean you want to use both channels 1 and 2 for both Tx and Rx, this is possible. In HDL Workflow advisor, you need to choose the transmit and receive reference design, and you need to select channel mapping as [1 2]. The same valid signal is used for both channels.