CODEC Support - Red Giant Bullet-Proof Understanding Ingest-Export Sequence Choices?

Question

I shoot with a Canon EOS C100 that records AVCHD internally. I also use a Ninja Blade to record DNxHD at 220 Mps. I find no built-in support for either of these formats in Bullet Proof and Premiere Pro. Is there a reason for that?
I'm trying to understand why the default export is MJPEG. For some reason, I thought that was an old codec no longer used. And it takes forever for Bullet Proof to export it. I have a very fast computer with an X99 2011 v3 chipset and 64 GB RAM, an Areca 12G RAID controller with a 16TB RAID 5 attached. And SSD for backup storage.
I don't mind editing MJPEG. I just don't know if it is the best I could do, or if it's better to edit the original AVCHD. In other words, If I ingest AVCHD footage, is it best to transcode it to MJPEG or another format for editing? Since there is no preset for AVCHD, what then should my edit settings be?
I also still do not understand the reasoning for the complex folder structure coming off the C100. I have read that it is important to leave that structure intact, but I don't see the benefit. Premiere has no use for it, it seems.

Answer 1

with the constant changes to adobe's software, its helpful to know which version we are talking about. alot of people ask questions here with older versions of the software... 
if premiere doesn't get your footage right when making a new sequence, then choose one that matches the footage the best by resolution and fps. you can also click on the settings tab, when making a new sequence, to customize it exactly to your needs. you can even save this as a preset that will show in the first tab with the default presets, so if you plan on using these media alot, you wont have to remake the custom sequence each time.
im not exactly sure what all you do in bulletproof, so i hinted at prelude since it does let you transcode to alot more codecs. prelude is an ingest program, you can trim clips (but only if transcoding), add metadata & markers, and have it export to multiple locations as the original and/or in different formats. prelude will only show presets when transcoding, so if you need a different one you will have to open adobe media encoder and make a new preset in there. then it will show in prelude. i like red giants software, but bulletproof export codecs seem rather limited. if the pass-through option just copies and doesn't re-encode then that might work for you.
when exporting from premiere you can also choose a preset close to your media and then customize it to your needs. you can even save it as a preset to recall later. i would stick with dnxhd for export, especially if you plan on bringing it back into premiere. dnxhd is very high quality if choosing its high bitrate format. there are several options for dnxhd 220, one should match your Ninja Blade. these are found under the quicktime format and video codec as avid dnxhd. its also available in mxf format.
adobe's presets try to cover a wide range of cameras and media but can only cover so many, new ones coming out all the time... in sequence settings and export you have full control to customize it to your media and needs.