Hi,
$1, $2, $3 etc represent the arguments give to the script at run time.
somescript.sh foo bar foobar
Inseide the somescript.sh script foo is assigned to $1, bar to $2, foobar to $3.
Although you can work with $1, $2 etc inside your script it is wise to use variables that are human readable.
Code:
#!/bin/bash
inFileOne="$1"
inFileTwo="$2"
if ! diff ${inFileOne} ${inFileTwo} > /dev/null; then
<some code>
else
<some other code>
fi
The above can be started as: scriptname.sh file1 file2
Do take a look at the Bash guides that are around. Here are 2:
Bash Guide for Beginners
Advanced Bash-Scripting Guide
Hope this helps.