Can I use the hardware serial and also use the com port created via the ide at the same time.
This question does not make a lot of sense. The IDE uses the COM port, set up by the operating system, to upload code. It does not create the COM port.
The Serial Monitor also uses that COM port, but not at the same time that the IDE is uploading a sketch. It does not create the COM port, either.
The other end of the COM port is what the USB to serial converter chip is connected to, via the USB cable, on one side. The other side of the USB to serial converter chip is connected to pins 0 and 1 (on other than the Leonardo).
You can not use those pins to talk to the GPS and the PC at the same time, unless you think that the GPS cares what you are trying to send to the PC.
If you post some code, we can help you understand what might be going wrong.