Apologies for taking so long to get back to this thread, I work very slowly and get very frustrated with how easy a task should be but how difficult I make it. Battery drain problem was the boot light staying on, the original earth for the amp was running to it and when I took it off, obviously I moved the switch so it didn't turn off when the boot shut.
Bottom line, after 2 incredibly frustrating weeks, the 6x9's are in the parcel shelf, not stealth but not bad and they work beautifully when the car is off, start the car and get the usual engine whining quite severely. Have researched a bit and I think the ground I have put it to might not be that good and the earth cable is possibly a bit long as well. I will experiment with this over the next week when I get time off but just wanted to let everyone know that I have appreciated the advice to date and will hopefully have a final follow up on the weekend.
If someone can just confirm for me, I am assuming the original earth that the aftermarket stereo goes to from the original loom is okay because the stereo has worked fine with no noises up until the amp and its earth was installed so as dodgy as this sounds, I will start with the earth at the amp and see how I go.