If you want your bundled application to run in the background — not show up in the dock — here’s what you do. Add
<key>LSUIElement</key>
<string>1</string>
(exclusive) or
<key>LSBackgroundOnly</key>
<string>1</string>
To your info.plist file. Use only one or the other.
LSUIElement will let you put up windows and dialogs. They’ll appear in the context of whatever application is frontmost at the time. If your process might ever need to put up an alert, this is what you should use.
If you choose LSBackgroundOnly, then windows and dialogs won’t work. Note that if you are writing a daemon, there are frameworks that you can not use!