If you just started SEO work with a new agency, you probably did some keyword research. You identified the keywords you want to target, found the corresponding URL, and ran some ranking reports to find the initial rankings.
If you simply copy and pasted the initial rankings with whatever rank tracking document you might use, you're doing yourself a disservice. For a large domain that hasn't had much SEO work and isn't greatly optimized, there's a good chance that the initial URL that's ranking isn't the URL you NEED to rank.
The dilemma here is that clients will see rankings that don't match the rankings for the URL they want ranking, which means that you likely won't see the improvements until your URL "jumps" the other. If you track the correct URL from the get go, the improvements you made will be appropriately accounted for, and you'll see improved results.
The only problem is you lose the automated part of the process, and tracking becomes more difficult. If you're like me and use SEOBook's Rank Checker, you know that the rankings they offer are always one to two spots lower than the rankings you see when you manually search.
I suggest changing the # of searches to the maximum allotted for each search engine, and Ctrl-F your URL up to 200 results. Figure out the ranking and drop it two or three spots, so when your URL eventually "jumps" the other one, you'll get a consistent picture of what rankings improvements occurred.
Hopefully the website you're working with won't have too many varied URLs that are ranking, so this task won't be too time consuming. If you want to speed up the process, only do it for Google, the most important search engine.
If you have any other suggestions to improve the process, I'd love to hear them in the comments.
Here's to getting full credit for our great work!