When you write, you write all bits in the register which are not read only. To change a single bit you will likely want to read the register, modify the bit and set it back. If you remember the state you had you could modify that value and write the register. If you are just setting a new state, you may not care what the previous value was and just write the desired value.
For example if you want to shut down, you might just write register 1 to 0x00 to turn off all FETs and use the longer sampling delay (FS = 0). Or if you were using FS = 1, you may want to write 0x80. Then write the shutdown bit in register 2. Here you want to stay in host mode so that it will shut down, so you would want to write 0x03, or you may want to keep your VGAIN and IGAIN settings even though you are turning off the part and they will go away when shut down is complete.