@ihcho, if pre #1 sounds better than $2 (plus has a phono stage), you could consider going without a remote (the horror!). If you just have to have it, do as you thought---tape out from pre #1 to any pre #2 input for phono. But your CD player should go straight into pre #2. Sending the CD signal through pre #1 gets you nothing, and may cost you a slight loss in transparency.
The addition of pre #1 poses no threat to pre #2, the power amp, or speakers, unless of course there is something wrong with it.