There are solutions for call tracking available that shouldn't negatively impact your SEO. One solution is to use an image replacement, another is to use javascript and figure out what type of source is referring the traffic and show an appropriate number.
How granular are you wanting to track your data? Do you just want to know direct vs ppc vs organic, or are you wanting to know each PPC keyword that drove traffic and which of those keywords converted? That'll affect the number of phone numbers involved and the cost.
For your local SEO, you will want to submit your regular phone number, not any toll-free number or tracking number. To the best of my knowledge, there's no good way to track the calls from people calling directly from the local SERPs, but you need those phone numbers consistent with all of the other published information that contributes to your NAP (Name/Address/Phone). Having the yellow pages with one phone number, other links with other phone numbers, and your local listing with yet a different phone number is a Bad Thing. Sorry I can't quantify it for you, I just know you want everything the same for that listing.
I hope this has helped. In a previous job, I worked for a company that provided call tracking and ROI solutions which is where I got some of this knowledge. I myself haven't implemented call tracking on my website, but I'm aware of a lot of the factors involved.