This post is 8 years old, might be time to revisit this research.
When you start to get frustrated with your simple home made bookkeeping system, check out this bookkeeping services comparison. I have used two of them, Cobalt and B2Bee, and experimented with trials on several others. In the chart below I have listed key criteria and what I could determine about how each service meets the criteria.
All of the services are internet-based. No software to install and update. Most of the services have more than one plan. For comparison the least expensive plan that allowed unlimited clients was selected for comparison. A general problem with these bookkeeping services is that the content/layout of the invoice is pretty static. You can customize the look but not the fundamental way the invoice works. None have a layout that supports a fee as a percentage of construction cost. You can 'trick' some layouts into showing phases and decimal quantities with unit cost equal to the value of the phase's fee, but you are on your own and may as well be using a spreadsheet invoice.
Here is the list of services and a brief statement about each of them. Bear in mind that I am an architect and not an accountant, and this is pretty subjective.
Nearly all of these services has some sort of limited free version or a trial version that allows you to try it out before having to commit. Even- after signing up, the majority allow cancellation at any time.
The table below is downloadable as a PDF which has hyperlinks to the services compared.