Arval, thanks for the questions. I'm going to address them, as well as your comment.
Perhaps this will facilitate trade and coin flowing without the employers being there 24/7.
Firstly, currently it's true that employers could walk away from the work without having to worry about employees being paid - they could even die and it wouldn't stop pay per hour because the total sum of money will already have been applied to the job.
However it may not stay like that forever, particularly with the introduction of facilities - a bank specifically.
I will be encouraging the growth of 'modern, civilized' societies by rewarding them with expanded options and passive benefits when the appropriate facility is built. I am still debating whether banks will be one of these facilities, and what effects it will have. Potentially in the case of a bank, without one, as an employer you must be in the location of your jobs in order for your employees to get paid and for work to progress. If a bank has been built in the area, you'll be able to leave the entire town, travel, do whatever you please, because the bank will distribute your money for you.
It's an idea I am still playing with as far as the connections with facilities and jobs go, so I just want you to be aware in case something along those lines occurs at a later date.
The goal is certainly to facilitate trade and build an economy. Workers will want to spend their money on goods, which will breed private businesses as well as community trade depending how what sort of town it is.
will there be different currencies or just gold?
On to your first question, the short answer is that I am not sure yet.
Here's the long answer. I have been discussing it and mulling it over heavily the last few days. It's all about balancing the economy between mechanics (characters will still be able to manipulate it if they are determined enough, but that's perfectly fine, and realistic).
Right now, I have money set as being mostly ambiguous, and using a decimal system which pretty much removes the need to have more than one type of money (mechanically, at least; the decimals could always be called something else, but the game itself sees it as just currency with no differentiation). I haven't decided yet if it's worth breaking it up into multiple money types. The question is simple, the answer is not.
It depends on the answers to several other questions about the economy. Will metal resources be limited? (Yes.) Will you be able to press your own metal into coins? Melt them back down? If we can melt gold coins should we be able to melt gold from items? What happens if, over time, all the gold is pooled into coins with none left for using in crafting? So on and so forth. An economy is a huge system with a lot of components, and I still need to work out the answers to all these questions aside from the first in order to get to the point of deciding how money itself is structured.
can resources used as currency in the pay system?
For your second question, the answer is no. You will not be able to apply resources or items as pay to an employee for their labor using the pay system. You can still barter for services and pay them in goods manually, but you will not be able to use the pay feature which will alleviate you from having to do anything manually at all. The pay system is automatic. The reason for this is that bartering is meant to be kept as a primitive form of trade, while the pay system is meant to be more advanced than bartering. Bartering with goods will never be as efficient or have as many benefits as trading with money. An additional benefit is that money doesn't take up inventory space, while goods do - a primary reason money began to be used in real life.
It will be encouraged by the nature of the system for potential leaders, town residents, and pioneers, to work toward building their town up to become more sophisticated and civilized in order to gain the benefits. They always have the option not to, and you could have a town that only believes/trusts in the bartering system, but you won't be able to use the conveniences that money (or potentially banks) will have.
Think of facilities a bit like the advancements in culture you can make in Sid Meier's Civilization series. Adding more sophisticated public works and technology gives residents more options, long-term benefits, or protection depending on the type of facility. They will help encourage culture, and along with the political system, will help define one town as being different from another.