Unless you have the TxData and RxData pins of your mcu linked to the PC either through RS232 or through an FTDI chip and USB, then you can't upload via the bootloader. But you don't need to, you can upload via ICSP instead. It shouldn't matter that you have already uploaded the bootloader. Use the same connections as for uploading the bootloader, and upload your sketch using the "Upload using programmer" menu option.
If you can't get it to work, try uploading the bootloader again to check whether your fuse settings are compatible with the mcu clock you are using. If you find that you can't upload the bootloader any more, then either you burned the wrong values for the fuses, or your clock isn't working - perhaps because of shorts on the crystal pins of the mcu or the wrong value capacitors connected to those pins.