I'm using a LilyPad Arduino 328 Main Board that has LilyPad LED Whites branching out from it. (about 18 of them, to be specific)
If you were to be specific, you'd show the code,so we knew where the LEDs were connected.
If you have any connected to pins 0 and 1, for instance, they will cause the problem you are seeing.
To upload to the Lilypad you can try selecting in the menu Tools, Board, Uno and see if it lets you upload. If that does not work, upload a photo showing clearly how you have the USB-to-serial adapter connected to the Lilypad.