For the mash and HLT, it won't matter where you put it if you're stirring the liquid or recirculating with a pump.
There are pros and cons to putting it in line as it leaves the MLT, right?
Pro would be you know the exact temp of the wort as it leaves the ball valve, but the con is that you probably are going to take at least a few minutes to bring the mash up each degree and unless you monitor the output, you may end up overshooting the temp as the element in the RIMS tube or the HLT water may heat the wort too high in an effort to bring the temp of the entire mash up. Not sure if that's clear, but you may end up heating the wort, at the small volume level in the HEX or RIMS tube up to 170+ as the system tries to bring the entire mash volume up.
I like P-J's way of maintaining mash temps with HERMS...set your HLT temp to a degree or two above your desired mash temp (or whatever it needs to be so your mash is where you need it to be and you account for the degree or two of loss in your plumbing as it leaves the HERMS coil). You'll can't overshoot your mash temp as a whole nor can you heat your wort too hot as it passes through the HEX.
But I know nothing about the BCS system or how you're planning to maintain temps...