When you install a PCIe GPU, the integrated GPU is automatically disabled to avoid a resources conflict between the two graphics adapters. This means you cannot use both adapters at the same time (unless, as on some newer motherboards) the BIOS has as option which allows you to do so.
You must connect both monitors to the PCIe GPU (if it supports two or more monitors of course).
You can find out if it supports multi monitors on the manufacturer's website, under that model's specifications details.
The integrated GPU will work when you remove the PCIe GPU, but that won't solve your problem with two monitors.