yamaha cx-1000u rs..can I run 2 subs?

Do you have preamp out? If so, what I do is run the preamp out to xover/amp for your sub and back. Usually you will see a jumper cable, if you have an integrated amp or reciver. I run the left cable to left sub, etc. On my minsystem I use a y cable or connector. I asume you are using a powered sub w/xover.

on my preamp I have cd,tuner,tape1/dat2,tape3,cdv1,cdv2,vcr1,vcr2,output1,2..I also have optical connections?Are these better ways to connect things?

We are basically talking about outputs. That limits you to basically the tape loop and the preamp out.The fact that you have output 1&2 is good. That maximzes your options. I assume the outputs are in stereo?

I also see phono jacks I missed.Yes the 1 and 2 output are stereo.I dont see anything on this preamp that says preamp out.And i'm not sure what a tape loop is.Forgive my ignorance.

If you are usiing a classic preamp you are covered by outputs 1&2. Some time ago makers of int. amps and receivers gave thier owners the option of using an outboard amp. You then could use the recvr.,preamp. along with a basic amp of your choice. The most common reason was for more power.
Before that many used the tape output/input for processor like equalizers. Thus you could feed the entire signal out on the tape out and back in. DbX expander was another device that could be used this way. You might be able to use your sub/amp/xover this way but be careful.