Okay,

To answer your questions (and before anyone says "I wouldn't do it that way", there are an infinite number of answers here!!).

Firstly some comments:
I will talk about Poser. It all pertains to D|S as well but Poser came along first (I am pretty sure) and it is hard work saying "Poser or D|S" all the time.

Runtimes are a mess. A complete pigs ear. This is a consequence of the development of Poser particularly. As each new version of Poser has come along the Runtime system has been tinkered with, bits added but nothing taken away. This is a (mostly successful) attempt not to break earlier content with new versions of Poser. Add to this that content providers put parts of their content (textures and the like) in random places. This is due to the above development of Poser and to the fact that there have never been any proper guidelines (well, there may have been but in mergers, aquisitions and development, they have "got lost" and there is nothing to enforce them.

Take ReadMe's (sic - should be ReadMes). These have no proper naming convention or location. Some put them in the runtimereadme's folder, some put them in the readme's folder at the same level as runtime itself, some put them in subfolders. Daz installers make HTML/text hybrid readmes. Its HORRIBLE!

Soo... rant over. What to do?

"1)Daz models are self-installing, should I place them in folders other than the poser or daz directories, as I have found that after a while both programs become very large and bloated."

Probably, yes. You need to decide how you are going to use this 3D program of yours. Are you going to major on one character? Are you going to use lots of characters? Will you be a BIG user, aquiring lots of content or will you stick to a more limited range of content and use it to its fullest extent?

When you have decided, then you can make the decision of how many runtimes you need.

I use only Victoria 4. I do have a lot of content for her though so I have several runtimes, one for each different type of content. I have one for clothes. one for shoes, one for poses (yes, one specially for poses to separate them from MAT poses associated with clothes/shoes etc), I have one runtime for V4 hair. Next one for non character specific props, one for botanicals and one for various animals (I dont have a lot of animals).

All this makes finding stuff somewhat easier but it is still a bit of a memory feat sometimes.

You might have runtimes for A3-Clothes, V4-Clothes, A3-shoes, V4-shoes and so on ad infinitum. Trouble is maky items come with stuff for multiple characters and where do you install it now? The answer is install it all twice in both (for example) V4-Clothes and A3-Clothes and go through and delete the V4-clothes out of the A3-Clothes folders and so on.

"2)Do I make runtime folders for each and every model? (Victoria three all files need to create the model would go into Folder V3, Michael 3 into Folder M3 ect) or should I place the main charcaters in poser and daz permanently?"

Your questions 1 and 2 are really the same and I think I have answered Q2 already

"3)Zip files - there is a lot of free models in Zip files do I make individual runtime folders for them too?"

Its up to you. If you think you might want to delete the content after trying it then make a runtime just for it and install it, test it. If you like it then install it somewhere permanent... say in V4-clothes (assuming it was clothes!!).

4)Do you only bring them (the models) into poser / daz as you need them, I mean say you want to make a city scene, with cars and people and animals would you only bring those items into poser as you use them for that project and once it is finished (the project), remove them from the content folder?

Some people make a runtime for each progect. A project being from one to a series of images using the smae characters and props. When they are complete you have a decision to make. "Am I ever going to want to resurrect this scene and chage it - or not?" If you might then you can either leave the project runtime on disk or burn it to a cd (along with the Poser or D|S scene files) and delete the scene files and the runtime from disk. This is a nice solution if you are at all organised. It is a bit of a pain making the runtime for each project. Again it depends on the kind of 3D artist you are - are you a prolific creator of loads of inconsequential scenes  or are you a careful crafter of a few very lovingly created scenes? If the former, then this system is not for you, keep all your runtimes on disk forever (just make sure you have a good system for finding stuff).

Some useful stuff. I have a program for sale here which would help if you regularly install content (who doesnt heh!) Particularly if you decide to go for the Runtime per project" scheme. 
Here is the link: http://market.renderosity.com/mod/bcs/index.php?ViewProduct=61876

Waldo Tim of dA has a great article on how he maintains his runtimes. He does it the permanent way and manually edits them - I wish I had his patience!
Link: http://www.yodelingyak.org/index.php?option=com_content&task=view&id=20&Itemid=1

Finally there is a GREAT program for layering any one of a number of schemes on top of one or a multitude of runtimes. It also loads content into Poser too. It is worth much more than he charges for it - which is $0 (or £0 where I come from). Use the latest beta.
Link: http://www.neocron.lunarpages.com/library/