Convert document color mode to Pantone/Spot

I have a document in which i have 2 layers, each layer contains shapes. one layer is supposed to be Pantone 293, the other layer is Pantone 296. right now, the colors are in RGB. I saved as is, then saved as PDF and the printer whom im sending this to, said the PDF printed out in 4 plates (CMYK) and i need only 2 plates, hence, i need the document to be in a spot color mode. How can i do this? How do i convert the colors i used in the shapes now to spot colors in CS3 version?

First I recommend changing the document to CMYK mode.
Here is the traditional fix: Window: Swatch Libraries: Color Books: Then select a Pantone Solid library. Show the Find field and type in your numbers. Double click the color chip to add it to your Swatch panel.
In the Swatch panel: Add Used Colors. To replace the global colors you are using currently, click on the Pantone swatch first, then the current swatch and select "Merge Swatches."
If you have lots of different shades of colors, you will have to create tints of the two spot colors.
Check your results using Window: Separations Preview to make certain you don't have CMYK being used. If your document is RGB, you will not be able to utilize Separations Preview (that's why I suggested the mode change)
You can also use Edit: Edit Colors: Recolor Artwork to make global color changes. But this is a somewhat complex dialog and takes getting used to. I recommend familiarizing yourself with this tool before using it in live production.

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