Keyword optimisation depends almost entirely on 2 factors: what your site is about and what you want to be found for. This is not something that can be done with software, as it is entirely up to your choice of strategy. Google WMT and analytics should give you more than enough information.
Once your site is in place, you can use tools to fine-tune things to profile your site relative to the competition.
You don't add keywords to the title of a page, or anywhere else for that matter.
Keywords are the "key words" for a page i.e. the central issue that page deals with. Those words should be mentioned in the relevant metatags as an indication for the bots that that is the subject of the page.
There is no such thing as keyword tags for the bottom of a page; all tags are in the head.
In general, keywords are the words that describe what pages are about, and the common denominator of those, is what your site is about. My site for example, is about "boiler repairs in south London" and almost all my pages have keywords related to that subject. Some page will have keywords like "brand boiler repairs" or "type of boiler repairs" or "model of boiler maintenance" (to avoid having to repair) and so on.
The importance of keywords in terms of SEO has changed massively. 10 years ago, you could bump your site by means of keyword stuffing and ramming your metatags full of them; this has gone the way of the dodo. In fact, if the algorithms find the amount of keywords too high/too artificial/too much out of context, you run a good chance your site gets penalised for blackhatting.