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

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.

yup seperate pre and amp..and I think I'm getting this now.So if I have two amps connected through my 1 and 2.Where would i connect a sub,or 2?I can use my tape 1,2 or 3 for this?

my first choice is to put it between the preamp and amp of the system sub is serving. Try putting it between output 1. As always turn everything off. turn volume down. Power up slowly. Stay near the volume control and on/off switch. Any thing that sounds amiss turn volume down and shut off immediately. Your subsystem should have some advice on this.