Is the gene sequence for these proteins known? You can try purifying these by proteomic approach if it is feasible in your system OR go for antibodies against these specific isoforms and study their roles in a probable signaling pathway in which they might be functioning. Try blocking those with small molecule inhibitors and see the downstream effect.
I assume that you with isoforms you mean alternatively spliced isoforms of the protein? And when you talk about using primers, you want to do RT-qPCR?
If you post the sequence of the two isoforms you want to detect I'll have a look and see if it is possible to design specific qPCR primers. Unless the sequences are extremely similar is should be doable...