All grounds need to go to bare metal, as in silver, if you can you should use a grounding lug, most companies (Tsunami, JL Audio, Stinger) make one. Having a poor ground ensures that you will not get the most out of your amp.
The Preamp input jacks on the 1000/1 are what you want to plug into, the inputs on the 300/4 (and all amps) are preamp inputs as well, the 1000/1 just calls them as such.
If you do not know this stuff like the back of your hand you should seriously consider professional install, 60 bucks is a lot less than the cost of replacing your amp.
Im not sure what you mean by cap. For two amps what i have always dun is run your main power and ground cables to your big amp. then from power and ground slots in your big amp just run smaller cables to the power and ground slots in your smaller amp. thats what ive done in my car and my girlfriends car and havnt had any problems with it at all. do the same with the remote wire too.