Changing from stain to paint

So, I built the Simple Cheap & Easy Console this past weekend.  I had previously done the Reclaimed-Wood-Look headboard (King) and used minwax walnut gel stain on it, as well as a neutral wood filler.  The filler took the stain really well on that piece.  With the table, I used the same wood (some of it scraps from the headboard, all of it bought from the same place), the same filler, but this time I used the regular minwax stain in jacobean.  It's horrible.  Hideous.  Splodges of really light areas where the filler is.  I'd googled around for fixes and ideas, and have tried all of them, including sanding down to bare and using the walnut gel stain.  No joy.  So here I am, throwing the towel in on staining it. 

My question really is - do I need to do anything to the stain that's on there before I prime & paint & poly?  I'll probably sand it all again and use MORE of the horrid filler because with paint I don't want any sort of 'character' to the wood, like I do with stain ;)  But other than that, anything I should know ahead of time?

Thanks for any advice! (except the piece about using wood filler exceedingly sparingly and buying a colour similar to the stain I'll be using...I've been yelling that at myself since sunday!)

Leah