So your question has several moving parts. Let me answer each one separately.

How were these wars financed and how was this money used? Where did the initial funds/resources come from?

These two questions are actually very interlinked, and you're actually asking an incredibly interesting question right now, so thank you for asking.

From the beginning of Christianity to the 11th century (abouts) there were incredible condemnations of usury, to the point where most interest and the payment of such interest was effectively banned. The main reason why the 11th century is highlighted is that European economic activity didn't really recover until this point (past the fall of the Roman Empire) to really support any sort of major lending activity, as an FYI. (Sylla, 68).

As such, people had to find extremely creative ways to get around the rules, and the fact that such bans had to be repeated again and again is pretty effective evidence that pawnshops and other such usurers were not uncommon in the early Medieval Ages, if not tolerated through things like Princely protection (Sylla, 70-71). We have also around the 10th to 13th Centuries an explosion of financial innovation, such as a return in deposit banking and the rise of banks as an institution. The earliest true "modern" banks - whether deposit, investment or the like - all date from about this period. Between the rise of the Italian banks (the first true one being established in 1157), the roaming groups of Italian Christians (usually the Lombrds, especially in the case of England and France) and Jews who served as bankers to all groups of people, and the rich (who were usually taxed excessively and then paid back in full later with interest as a consideration for such treatment, forming a type of psuedo-loan) there were multiple channels through which any ruler could effectively finance their wartime activities.

Further introductory reading

Sylla, Richard, A History of Interest Rates 4th Ed.

Kindleberger, Charles P. A Financial History of Western Europe

Moore, TK. Credit Finance in the Middle Ages

(Let me know if you want more history of finance stuff - I have lots, haha)

How were they paid off in a system where many didn't even earn a wage in any modern sense?

Government borrowers, no matter what time or point in history you're talking about - including today - have several special powers that regular borrowers do not, which include of course the ability to tax their residents, to destroy institutions and raid their money, and finally the ability to change the exchange rate of their currency (this last one is considered a form of crisis or default through debasement). Finally, they have a unique ability to effectively force default, in a way where they could re-enter the markets (albeit with some trouble) not too long after (though this is not always the case). All of these, of course, include a whole slew of cost-benefit analyses, since any of these if done inappropriately would cause a huge uproar.

In fact, however, the financial burden on both countries were so great that it caused one of the first financial crises in (modern) banking history, when Edward III of England could no longer pay back his Florentine loans, triggering the first international debt crisis and one of the first modern bank runs. And whereas England was off triggering defaults both domestically and externally, France was debasing its currency left and right, with a handy dose of extraordinary instability in its economy, mostly due to these sorts of wars. The record was probably when they debased the silver content of their coins by 50% in 1303, lmao.

Finally, there was the ability to tax. While you're right - people didn't "earn", per se, as they do in the modern era - there are two main methods of taxation just in general: direct (that is, assessed on the people, with the "people" split between laity and clergy) and indirect (taxes on goods, services, etc.). Even at the direct level, however, it was mostly communal: people paid taxes as a group per settlement based on rates established by Parliament. For clergy, that was income generated from their office.

Finally, for indirect taxes, it was taxes on products - things like wool, sheep, etc. This was probably the more important of the two sources of taxable income, as most average peasants depended on the sale of products for their livelihood - wages were probably extremely uncommon (Wuetherick, 31), and it was during this similar period that merchant fairs, where large amounts of products were bought and sold, were at its peak. Especially with the rebalancing of exactly who was paying the debt burden, with the government coming up with creative ways of ensuring that some of it was also enforced on foreign merchants (especially through wool export bans or increased wool taxes).

Further reading

Wuetherick, Bradley War, Economy, and Society: The Impact of the One Hundred Years War in Late Medieval England

Reinhart, Carmen & Kenneth Rogoff This Time is Different

http://ramscholar.openrepository.com/ramscholar/handle/10675.1/17