Check the help files on GetParameterAsText (or sys.argv in pure python) In your script you will set your input parameters as such, then in the toolbox, you give it the type. For example, here are snippets from one of my scripts and how I establish the association between the inputs and how the tools parameters need to be identified.
'''
Properties:
(right-click on the tool and specify the following if creating your own tool)
General
Name mxdInfo
Label mxd Information
Desc Project information focusing on table of contents and data therein
Parameter list
Parameter Properties
Display Name Data type Type Direction MultiValue Dependency
argv[1] Select a project Arcmap document Required Input No
argv[2] Output textfile Text file Optional Output No
argv[3] Include env ... Boolean Optional Input No
'''
....... The above is part of the header section, the next is the first few lines of the actual script
import sys
import arcpy
import textwrap
arcpy.env.overwriteOutput = True
#for toolbox
mxd = sys.argv[1] #Notice that sys.argv[1], or arcpy.GetParameterAsText(0) is a project
output_file = sys.argv[2] #sys.argv[2] is an output text file
envBoolean = sys.argv[3] # a Boolean indicating whether environment variables are to be included
