can easily put it back into my XP tower and reformat it using the FAT or FAT32 command, will my Amiga see the HD then do you think?
No. PC file system does not affect AmigaOS at all.
I have a spare IDE Secondary that I can use
As always, all the needed details are missing. I suppose the "spare secondary" refers to the second channel of a 4-way IDE adapter. What kind of 4-way adapter is it ? To access the second channel a special software is needed. Which software do you use ?
If you use the IDEfix software, there are two parts of it. One is atapi.device and one is the IDEfix program itself. To access a CD or DVD drive you can use atapi.device and don't need IDEfix. But to access a HDD you have to run the IDEfix program, otherwise devices on the second channel are not seen.
Check HDToolbox' tooltypes. If there is one beginning with SCSI_DEVICE_NAME=, make sure that it reads SCSI_DEVICE_NAME=scsi.device. Otherwise HDToolbox will not scan the correct driver.
Also remember that you have to set the jumpers correctly. The can only be one master and one slave on each channel. Two masters or two slaves on the same channel lead to corruption and data loss.
Also make sure that the IDE cables are connected correctly. Especially if you mix 2.5" with 3.5" devices. Although there are two 3.5" connectors and one 2.5" connector on the IDEfix adapter, you can only connect four devices. The 2.5" connector and one of the 3.5" connectors are shortened, they belong to the same channel. So if you use the 2.5" connector, only one of the 3.5" connectors can take two devices, the other one holds the slave of the 2.5" connector.
Bye,
Thomas