That's just the nature of wood. The two different colours may be because the blank the stock was made from was part heartwood, part sapwood. Is one part creamy white, and the other a more pink shade?
I think most people just accept that as part of the natural beauty of wood and use one shade of stain all over, allowing the colour difference to show through the final finish. I'm not sure how easy it would be to try and stain it to a single matching colour, or how successful the result would be?
Having said that, it's your stock so do it the way you fancy, and if it works it's a lesson for all.