And which games are you patching and for what system (NES; SNES, etc)?
When you press apply IPS patch you need to first select the IPS (which you download from this site, and then you need to select the original ROM, which you need to find your self on the net). After patching the original rom will be transofrmed into the modified rom (hack).
You need to check the CRC of the original ROM to patch to and if it need a header or not.
For instance for Super Mario World for SNES - original ROM can be US, EU, Japan and each with header or no header. A patch works only on one, usually US with header. So if you have no header it will not work, if you have Japan version it will not work etc.
Check the CRC-32, listed with the hack under ROM/ISO info, then check for header or no header (200 bytes at the beginning of the file) under patching info.
Also, this is definitely for newbie section of the forum.