I bought a Masterbilt Epiphone DR-500mce largely because of it's magnetic / undersaddle pickup combination. The blended sound is perfect for my jazzy pop fingerstyle playing. I recommend this approach regardless of how you achieve it equipment-wise.
One thing I had to do was change they type of strings I use. I had been using Elixers for years, but I found they were too soft through the magnetic pickup. Coated D'Adderios give me a much better blend between the two pickups. With a custom system, you probably will have more flexibility in terms of boosting the output from the magnetic pickup, but it still might be something to consider.
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