Hi Pete,
I've found the best source for the velcro to use for mounting patches on a current issue Nomex flight jacket is from a company I found in the US on the web.
Williams & Williams - Flight Suit Name Tags at
www.nametags4u.com
They have both the hook (which goes on the back of the patches) and pile (which goes on the item of clothing) velcro fasteners in a range of colours and pre diecut shapes. They also have velcro in 'bulk' strips.
Normally the patches would be sewn on using nomex thread or in worst case cotton thread - not polyester or nylon based thread which would represent a risk to the integrity of the Nomex clothing in a fire.
W&W also do customised name tags and have a range of patches.
Quite often the patch suppliers will offer a patch with the hook velcro and the pile velcro pre cut to the shape of the patch and with the patch sewn onto the hook side of the velcro 'as supplied' as an option. Makes it much easier.
Protocol for patches for USA or USN, best bet is do some Google image research for images showing current aircrew so you can see how they place patches. If you are looking for a particular unit layout, that might help as well. But the arrangement seems to be name and wings patch left chest, command or major unit right chest, US flag left shoulder with stars to front edge, unit or aircraft type badge right shoulder. Although you can find the occasion variation to that.
Other Air Forces use similar protocols for layout of patches on clothing.
HTH
Regards,