You can configure TeXlipse to use a custom script through the following steps:
Method 1: Script as part of the build process
This method will include the script as part of the build process, that is, you need to tell TeXlipse to build your project via Ctrl + B, then your script will be executed.
Go to Project > Properties:

Select the Builders tab and then click the New... button:

We need to choose which type of builder we want. Select Program, then click OK:

Now, configure your script accordingly (sorry for the shameless self-promotion here):

Our new tool is now listed in the Builders list. You can check/uncheck the builders you want to use:

Now, we just need to run it through Project > Build all or via Ctrl + B:

We can see that the tool was correctly executed (I wrote a dummy directive to force arara to raise an error):

Done. :)
Method 2: Script as an external program
This configuration only sets your script to be manually executed through the Run button.
Click the Run button and select External tools:

Configure your script accordingly:

And now our tool is available in the Run button:

Hope it helps. :)
Both methods are project-based, so you need to replicate these steps in other projects.