You are right. Greater connectivity is definately an advantage of Modbus as almost any industrial device supports it. But I think that its main advantage is that it is old and thus well tested and documented. Plus its newer versions, Modbus Plus and TCP/IP, allow more flexibility in control systems. You can find plenty information about Modbus on the internet.
Now to your problem.
Master needs both query and response algotirthms. But slave needs only to answer. Are you using Modbus or are you creating your own protocol?
Your question is not completely clear to me, but here comes the answer anyway while refering to Modbus.
Suppose that a master sends a message to a slave. The message looks something like this:
Header (e.g. :01B1F5.... the header is a colon as you see it in a hex file)
Slave address (e.g. traditionally modbus supported 0-255 devices)
Function (e.g. read/write register, set/reset bits etc.)
Data:
Starting Register Address (High Byte)
Starting Register Address (Low Byte)
Number of Registers to access (high byte)
Number of Registers to access (Low byte)
CRC check
3.5 character time (e.g. the end of message indicating a new message can begin)
So suppose you want to read contents of 4 registers starting from register 0201 decimal (00C9 hex).
In Modbus Data field you would write:
Starting Register Address (High Byte)=00
Starting Register Address (Low Byte)=C9
Number of Registers to access (high byte)=00
Number of Registers to access (Low byte)=04
When a slave receives this message it will read contents of 4 registers from 0202 to 0205. Note that with Modbus convention when you specify register 0201, Modbus will read 0202. (It always increments register address once).
To answer your last question:
When the slave responds, it will send function code back, number of bytes and data (high and Low bytes) of each register back to the master.
So in this case, it will send 8 high and low data bytes from 4 registers.
My experience is based on Modbus and I would recommend you use it as a guideline or when you get stuck.