Some Mystery Writing Rules:
Here's an important link to review before you get too deep into your plotting: http://www.mysteryinkonline.com/2005/01/twenty_rules_fo.html
You've got to make sure your mystery is fair. After all, you don't want your readers feeling cheated at the end of the book. Actually, if you have a potential editor or agent feeling cheated, your book won't even get as far as a reader. So keep it fair. Most readers like to match wits with your sleuth.
Some Mystery Writing Tools:
I'm in brainstorming mode now. Right now I don't have my suspects fully formed. In fact, I haven't even decided on their names. But my plotting is starting to make some inroads. One tool I use to organize the masses of paper and typing is a free one you can find online: http://freemind.sourceforge.net/wiki/index.php/Download Included is a Wiki that tells you more about the product. Basically, you can use it to create a visual outline. To see screenshots of some example FreeMind maps, look here: http://freemind.sourceforge.net/wiki/index.php/Main_Page#Screenshots
My FreeMind map has the name of the mystery in the middle. Coming out of it are "Suspects for First Murder, "Suspects for Second Murder," "Scene of Crime" (with 4 nodes coming out--Place, Clues, Weapon, Body), "Sleuth," "Victims," "The Killer," Setting,"--you get the idea. You could do this on paper, too, of course. Might want to get a big sheet, though. Each node has more nodes coming out of it with more information. Out of the "Victims," I have 2 nodes--one for each victim. For each victim, I have suspect nodes. It helps me to see how it all fits together.
Another bit of software that I like can be found on this UK site: http://www.writerscafe.co.uk/ . The software creates a bulletin board with index card look for your story. This is very helpful in keeping up with your different storylines. This is not free software (and the dollar to pound exchange rate is not the best right now), but it's not too expensive, either. 
For all you moms out there: is school still out where you are? If so, it might help you out to make yourself a schedule. At least you'll start out with a game plan (every good mom knows that plans have to be flexible!) Right now I've got my going-into-middle-schooler on a Whitewater rafting trip, but my 6 year old is home. My day looked like this:
Coffee. Take out dog and get/read paper. Check email. Work on my plotting for 30 minutes. Fix breakfast for my daughter and some for me. Start a load. Write a blog entry. Make sure daughter is dressed and has done a little tidying up in her room. While daughter is playing, do some research online. Run a few errands (gas, purchase and send a gift) and come back home. Put laundry in the dryer and prepare lunch. After lunch, write for a few more minutes. Take daughter to the Kitt Kittredge movie. Make supper. Run load for a couple more minutes to de-wrinkle. Hang up laundry....
The important thing out of all the drivel above is that I did schedule some one-on-one time with my daughter. She can put up with almost any amount of distraction from me (and even my telling her that I do need 30 minutes alone....bye-bye) if she knows that we are going to do something special together. Many times we just play Memory together (a game I'm abysmal at) or read stories. But the time is there and I make a point of making it. That way I don't feel guilty when I'm carving out time to write.
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