In day to day terms, managing a building site is somewhere between a science and dealing with a madhouse full of demented jugglers, especially if you have never done it before. Partly this is because of the number of variables which can occur. Consider using a project manager, a self build consultant or a clerk of works or possibly a friend who has experience in the business. They should be able to bring a wealth of information to the project.
A clerk of works is probably best employed to make regular inspections as the work goes along. They will report and help sort out any problems. There is a description of work undertaken by site inspectors on their institute web site. (which could do with a bit of updating at present)
If you take on doing the self build management yourself then the best strategy is to be very well organised, have recourse to professional advice when you need it and then to have a set of fall back positions with their interdependencies worked out in case things go wrong. On a good day everything proceeds well; on a bad one at least you achieve something useful and don’t come to a standstill.
The NHBCThe National House-Building Council describes itself as being "the leading warranty and insurance provider and standards setter for UK house-building for new and newly converted homes" do a Technical Extra which gives a breakdown of the commonest problems that arise in insurance claims.
On a larger scale of thinking, especially if money is tight and there is a risk you might not be able to afford to complete the house for some reason, it might make sense to have clearly defined intermediate stages where you could sell the partly completed project for a price which reflected the cost and effort which had gone into it. Typically this would be when the building is weathertight and secure or at the point before the internal finishes go in. At these points a potential buyer can see clearly what they are getting and how much they need to do to finish it. This is a strategy much used in Scandinavia by young families who are self building. If things go wrong and they have to sell up before completion they at least make a small profit. A building with half its roof on is not an attractive purchase.
Project management software is a good bet. Many self builders get by by using computer spreadsheets for all the small calculations needed. This is fine but gets a bit clumsy when there are lots of them and it doesn’t allow for a Gantt chart (where time taken to do a particular part of a job is displayed as a timeline bar – so that you can see which jobs overlap with each other). The free US software is ahead of UK software in this respect but is mostly irrelevant because building regulationsThese are the legal regulations which govern how a house is constructed. (not to be confused with Planning Permission which is about whether you are allowed to build the house at all or what it might look like) see Building Regulations) are different, manufacturers and suppliers are different and customs are different. Avoid US management software. Some UK software is tied back to a particular builders’ merchant so you may get a bit compromised using it.