Working with big lists of keywords...The first step is to cut out the crud.
Then, divide the rest into three groups:
Best - Should rank well in all three factors:
1. Popularity of keyword (demand)
2. Number of competing sites (supply)
3. Value (are other webmasters spending money for the search term?)
Take your best 10-30 or so. You will want to hammer away at these, almost every page you have should contain these keywords in some combination.
These are the keywords to feature in page titles, internal and external linkage, domain names, URLs/File names, etc.
Good
These should be solid on the three categories above, but nothing that really jumps out at you.
A good niche should have 50-200 of these keywords. Sprinkle these in liberally with the BEST keywords.
OK
These keywords should have decent #1 and/or #3 from above. Some would call these the "longtail" keywords.
A decent niche may result in 100-1000 of these. Use these more lightly but try to get at least an instance of two of each somewhere on your pages BUT NOT AT THE EXPENSE OF BEST AND GOOD KEYWORDS.
Next, we need to "weigh" these keywords. I don't know what keyword "index" you are using, so I can't be specific, but in general follow these guidelines:
If one keyword has a "rating" of 100, and another keyword is rated 10, that makes the first 10x more powerful. ( 100/10 = 10 )
Therefore in theory, you will want to use the better keyword 10x more than the second keyword.
The same strategy should hold true...If one keyword has 1,000 searches and another has a rating of 50, use the first one 20x more often, as 1000/50 = 20.
Again, this is theoretical, as weighing keywords like this exactly proportional across all your pages isn't "conventient".
However, if you see one keyword is rated as 1000 and another as 50, you know you should use that keyword a lot more than the other keyword.
-Boom boom boom boom.