I have been trying to integrate a satellite dish for foreign stations into my existing cable setup. I read that a RF modulator would enable me to shift the output to a channel not being used on my cable system but whatever channel I try my cable boxes will not allow me to tune to that station. I'm using 94 and it works on 1 TV that does not have a cable box attached.
What am I missing?

I can't say that I have heard that. I would try connecting to a different input on my television from the cable. Say video 1 vs. video 2.

Above would be a good solution, if for 1 TV.
If for whole house you will have to get a Trap that will go inline with the incoming Cable. One that will trap a range that includes Channel 94(Program Modulator for different channel should Cable channel 94 be a channel that you like).
So on the cable input to Trap this will go backwards into a 2 way splitter, the other wire that goes backwards in the 2 way splitter is from Sat, through Modulator, outputting channel 94? Now you have the Single Output(It is normally the Input/ You can use a splitter to split or join). Have it connect to a 3,4, 5 way splitter , and amp first if needed.
Do you use Cable Boxes in the Rooms? Is it digital?

I have the system set up that way. The problem is that while I have two televisions without cable boxes and they work fine with 94. The televisions that have cable boxes don't work because I can't get the cable box to tune to 94. There isn't anything on the channel. It seems the cable boxes will only tune to the channels the cable company provides. Is there a way to get them to tune to 94 ? I do have digital cable.

The 2 locations with Cable Boxes, I would have a 2 way splitter from wall(or double coax in wall plate/splitter in wall) and have 1 output go into Cable Box. Would be nice if you're NOT using Coax to TV from Cable box (Composite, component, anything)then the other output from splitter could go to Coax in on TV.
Then On the TV, you would select Video 1(2,3,4 or whatever) for Cable, and Channel 94
For FTA or whatever.

Couple other thoughts come to mind, How is Cable box in rooms connected to TV?

To answer the original question: No, you can't change the channel mpping on the digital cable boxes. Most cable companys use the Motorola DCT's, and they can only be changed from the system that they use to send hits to the boxes for activation (probably a DAC)

If they ARE the motorola boxes, do they have an RF bypass? By which I mean, if you turn off the DCT, can you still change the channel on the TV and get cable? If so, then you would just need to turn the box off and change the TV to 94.

This can be done with 1 cable.

Can you tell me how to do this? By the way the rf modulator I'm using can be configured for a number of different channels. The main problem I'm having is getting my tv's connected to explorer cable boxes to recognize the added channel.

Please, are you using 1 cable(coax) in or other A/V signal to TV?
You may be able to have in rooms with cable box, splitter at wall, 1 in to cable box, 1 back to a 2 way splitter backwards, then have output of cable box to splitter, common to TV. Then Select 3? Or 94.
If box is putting out signals close to 94 frequency, then a filter is needed.

You can do it but you need to use a Logenex SCFM modulator and may need diplexers or just regular splitters. It works a treat but it is not cheap. Probably around $400 to $500.

Check out logenex.com call them and they will help you out.