Add a modified week view.
One week is showed as 7 elongated rectangles, graduated by hour (major) and quarter hour (minor) along its height, and hours worked per job are represented by rectangles of a particular color. The day starts at the top at a user specified time (default 6:00am) and graduated past midnight of that day and onto 5:45 of the next day. As hours are recorded, they are plotted as rectangles from clock in to clock out time. Each job gets its own color, and if hours overlap, the job clocked in first gets justified to the left, second (third,fourth) gets justified increasingly right, giving a staggered view of the overlapping time. At the top of the column would be a text summary, total hours worked in all jobs that day, and hours worked per job.
Again, a mockup would really help here. This one sounds pretty complicated but I'd like to get a visual to understand what you are describing.