I'm not sure I fully understand what you are saying or asking but if you want to control aMule using scripts, amulecmd is a really handy tool. Since version 2.1.0 we are including amulecmd with our binaries. It's in "aMule.app/Contents/MacOS/".
For example, the following 'aspeed' script allows me to control aMule's upstream bandwidth, which is particularly when I want to access my machine remotely via vnc. Before I connect via vnc I do a "aspeed 20" over ssh to reduce aMule's upload speed to 20k/s. Very handy.

#!/bin/sh
/Volumes/IncomingHD/-amule/aMule.app/Contents/MacOS/amulecmd -c "Set BWLimit Up $1"
To get an idea of all of amulecmd's features, just start it via "/PathToaMule/aMule.app/Contents/MacOS/amulecmd" in the Terminal (you need to set up remote connections before in aMule) and type "help":
aMulecmd$ help
Available commands:
Add Adds an ed2k link to core.
Cancel Cancel download.
Connect Connect to the network.
Disconnect Disconnect from the network.
Exit Exits from the application.
Get Get and display a preference value.
Help Show help.
Pause Pause download.
Quit Exits from the application.
Reload Reloads the given object.
Resume Resume download.
Set Set a preference value.
Show Show queues/lists.
Shutdown Shutdown aMule.
Statistics Show full statistics tree.
Status Show short status information.