First: if your parents tells you that it's making your computer "run funny", they are probably right. Bit-Torent can take a lot of ressource, especially if your downloading and uploading limits are not set. Try to lower them, at the very least it should make their internet surfing faster since the computer won't always be at the limit.
Second, you can go in the options like you said and set it so it's always hidden. If they open the icon bar they'll see it running, but if they don't they won't notice.
Third, there is options in Bit-Torrent to decide what happen when you minimize the program. I know there is one option to remove the icon when the program is maximized, but I removed it because it was buggy (the icon bar never colapsed back whenever it happened). There is 3 options, did you try experimenting with them?
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