Question: Well, I do know that for a single script the question is to just put the corresponding file in directory `/etc/rc.local`, right? But, what if this script depends on other files (i.e. a few scripts and a couple of text files)? What should I do in order to avoid making this certain folder a mess?

Answer: 
If by **depends**, you mean it **uses and/or calls** them, that **should not matter**. You can just add a line to the end of the rc.local file as a command to call the main script and it **should just work**. 

There is an **alternative to rc.local**, atleast on desktop versions. You can use the **`Startup Applications`** app to add your script to it. The difference between the two methods, other than CLI vs GUI version of adding is that **rc.local scripts** are run as **ROOT** and the **startup applications as your user**. 

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### Edit

From the comments, your problem becomes **clearer**. It seems that the script is using **relative paths** to access the dependency, which I'm guessing isn't code. The working directory of the above two methods are either `/root/` or `/home/<user name/`, thus the **dependencies dont load**. 

Easiest fix is to **`cd` to the folder** before invoking the python script. Either of these should work:
- Use `cd /home/..../.../ && python perdc_task.py` as the command in either of those two methods.
- If that doesnt work, make a script(`.sh` should do) which calls the above command and call this script in the above 2 methods.

The more elegant way of doing it is
- Do the `cd` from **inside the python script** by programatically determining its path
- Or Use the above path to access the dependencies by **absolute path**

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### Edit2

Ubuntu might have moved away from rc.local in favor of [upstart](http://en.wikipedia.org/wiki/Upstart). Try to see if using upstart as in [this question](https://stackoverflow.com/questions/7783341/run-script-with-rc-local-script-works-but-not-at-boot) works for you.
If you have `cron` enabled (which you should) there is a special `@reboot` command which runs on startup. I am unsure of this works on cold boots though, but from what I can see it does.

If it works, you just write a script, plonk it in some clean and organised directory, then call it through `cron`.

See: [Here](http://www.cyberciti.biz/faq/linux-execute-cron-job-after-system-reboot/) and [Here](https://help.ubuntu.com/community/CronHowto)