There are many tutorials on ISP programming but unfortunately it remains a somewhat confusing topic. Most tutorials cover using an ISP programmer or another Arduino as an ISP programmer for the purpose of burning a bootloader. Few of them cover uploading sketches that way. And the ones which do are often outdated since as of IDE 1.6.5 the Upload Using Programmer option moved from the File menu to the Sketch menu. If you find a tutorial you like for using ISP to burn a bootloader, near the end where it says to go on the menu to Tools, Burn Bootloader, you can skip that and go on the menu to Sketch, Upload Using Programmer.
So look here first:
Skip step 2
when you get to step 7, which is confusing and talking about burning the bootloader, do Sketch, Upload Using Programmer instead.
Here is a short tutorial about uploading sketch with ISP:
It is a little outdated because it talks about the Upload Using Programmer option being on the File menu instead of Sketch menu.
If you upload sketches using ISP, you will no longer be able to upload with FTDI, because when you upload using a programmer it erases the bootloader. You can put the bootloader back on it using ISP programming and the Burn Bootloader option. That was a nutshell version...
I have an overview of how the uploading process works, including FTDI and ISP, you may like it because it has a lot of detail: http://www.instructables.com/id/Overview-the-Arduino-sketch-uploading-process-and-/