sumghai

AFAIK, that is exactly it - you add a docking port to the cargo bay, which docks to the corresponding port on the probe you want to capture, and then you close the bay doors around the probe so that you can timewarp / re-enter the atmosphere safely.
No, the cargo bay isn't a spawn point for payloads.
One would usually build the payload first, then manually add the cargo bay around it, and finally building the rest of the "launcher" craft.
Alternatively, build and save the payload separately as a subassembly, to be inserted into the launcher craft in the VAB.

Please don't copy and paste the entire log file into your forum post, as it makes your thread very hard to read. I've put the log file contents into a spoiler block, but in the future, please upload your log to Pastebin, and link to the uploaded paste in your post instead.
Looking at this section of the log:
Unity Player [version: Unity 4.6.4f1_99f88340878d] mono.dll caused an Access Violation (0xc0000005) in module mono.dll at 001b:10107259. Error occurred at 2016-05-29_111232. C:\Program Files\Steam\SteamApps\common\Kerbal Space Program\KSP.exe, run by Lyric. 80% memory in use. 3327 MB physical memory [645 MB free]. 0 MB paging file [0 MB free]. 2048 MB user address space [56 MB free]. Write to location 00000000 caused an access violation. The first line mentions Unity 4.6.4, which indicates you are running an outdated version of KSP, 1.0.5 or earlier. Old KSP versions like 1.0.5 are 32-bit applications, and so can only used a maximum of 3.5Gb of RAM before running out of memory and crashing.
Further down the line, it states that you have 3327 MB physical memory (645 MB free). That is the total physical amount of RAM available on your computer, which is used by both your computer's OS, various background services/programs and KSP.
You're experiencing frequent crashes because quite simply, your oomputer does not have enough RAM to run KSP.
Recommended Solutions:
- Buy more RAM for your computer (or better yet, buy a new computer altogether)
- Update your game to KSP 1.1, and run the 64-bit version KSP_x64.exe instead (the 64-bit version is able to use more RAM)
 

@bigsilverhotdog, I never asked you to test each add-on in isolation. Please don't misquote me or take my statements to the extreme to vent your frustrations.
What I'm saying is for you to start with an unmodded game, add one or two mods at a time, check that they don't cause any major problems, then add a few more and repeat the process.
Bear in mind that for KSP 1.1, SQUAD migrated to the Unity 5 engine, and practically all plugins required recompilation - this is a major change from 2013~2014, when KSP was still based on Unity 4.6.x.
While CKAN is a convenient tool (which I myself use), it is poor practice to hurriedly install suggested mods without understanding fully what they do.
CKAN listings for each mod are not necessarily maintained by the original modders themselves, so there are bound to be entries with insufficient description. So basically, if in doubt, don't install it until you've read the manual / thread describing what the mod does.
Edit: I should also add that while a mod author may have updated his/her mod to KSP 1.1, it takes time for the updated version to propagate through CKAN, since it (again) is often maintained by third parties.