Hi, soap4u, and welcome to the forum!
Hmm, if you've got soap chunks, it sounds like maybe your base had not melted all the way before you poured? I know I frequently have to gently stir for a bit to break down reisidual chunks after microwaving. Be careful with your stirring, though -- if you stir too quickly, you'll whip little bubbles into your soap. You can nuke it again, but it just takes that much longer to cool it back down, and you might scorch it.
It's hard sometimes to see or feel those chunks when you're stirring, especially if it's an opaque base. Move your spoon through the base slowly and really try to see or feel the chunks. It's easy to miss a few small ones.
If your base is fully melted, it shouldn't get chunks in it while you're waiting for it to cool enough to layer. It might get a skin or feel like it's turning to gel if it gets too cool. My guess is that the chunks are bits of soap that didn't fully melt in the microwave.
Good luck! Let us know how it goes!