For the longest time I've been using both xNormal, GIMP & Photoshop together for baking and texturing. I'm still a quite moderately mediocre in texturing, just mentioning it here now.
Mostly, I've usually baked without padding and added it later with xNormal's PS plugin, depending on the texture (for example, the baked normal map is usually untouched because it's already done, so I'll usually bake it with padding). Sometimes I'm getting visible seams even when having padding added. I think the reason is that I may have decreaced the size of the texture from 4k to 2k or something, and alpha borders of the UV islands get blurring.
But still... my texturing workflow is really messy. Sometimes I bake with padding and sometimes not. xNormal's plugin doesn't pad more than 32 pixels at a time which is tedious to re-apply it to get "infinite" padding which is ideal. When baking in xNormal, I guess the padding limit is 192 pixels or something. I think it should be infinite.
Also, the problem with current GIMP 2.8 is that it doesn't support 16-bit images. It always converts them to 8-bit when importing. In case of normal maps it doesn't dither them, so visible and nasty banding can be expected when viewing in a normal mapped model in a game engine. That's why I dither them in PS.
GIMP is still quite good with other texture types apart from normals, and I found this very nice plugin just a month or two ago: http://polycount.com/discussion/114616/uvpadder-filter-for-gimp-2-6
But, I've been waiting for GIMP 2.10 which is WAY better in many ways. Such as the 16-bit support. But... the development is too slow at the moment, so... summa summarum, I literally JUST bought both Marmoset Toolbag 3 and Substance Painter 2, to get rid of xNormal, GIMP and PS.
So, as a beginner with baking in MT3 and texturing in SP2, I'd like to know what is the best way to handle the bakes/textures in either of them? In the end when viewing my textures in a game engine, I've always used 8-bit textures though. Just for optimizing.
* Baking with 16-bit .tiff with or without padding?
In SP2 you'll have this option when exporting you maps:https://support.allegorithmic.com/documentation/display/SPDOC/Padding
But you can also pre-dilate them (dilation width setting) when baking in SP2 as well:https://support.allegorithmic.com/documentation/display/SPDOC/Baking
* Can SP2 work with 16-bit stuff?
As I'm a character artist, I'd also like to bake the thickness map for the skin. So, SP2 seems to be the only one supporting it at the moment. MT3 doesn't support it. But think I'll bake everything else in MT3 though.