All of these factions are trying to stay secret, that doesn't mean they leave no marks upon the world or cannot be interacted with by outside factions like the PCs.
Know What's Going On
First, it's important to keep track of characters within the secret societies, what they are doing, and what they know. GMing often involves some degree of abstraction and improvisation. How much varies by GM and game. If your campaign relies upon secret society investigation, then you need to be tracking the “shadow plot” that your players don't see directly.
Having a solid grasp on what's happening in secret will help you to apply the techniques below.
Every System has Cracks, Every Person Has Flaws
The Masquerade may get treated like an absolute law, but that doesn't mean it gets perfectly obeyed. Once you have a group of people with problems and passions, it gets hard for all of them to behave perfectly. Someone will frenzy while hunting, someone will spill the beans to a human they care about, someone will leave objects or information in places they shouldn't. Strange bodies turn up. City politics start getting weird, and local businesses look fishy.
Most people, especially in the World of Darkness, go through life with blinders on. They are worried about their own problems, and are ignoring the big pictures. This means that secret societies can (and do) have a lot of small slips and even a few moderate breaches while still remaining fairly secret. Your PCs are special because they are looking closely at things and trying to put the pieces together. Plenty of evidence should be there for them to find once they start looking.
The Flaws Are Beautiful
As a GM you cook up schemes and plots. You know how the villains, the secret society members, the others, are going to stay hidden and pull off their amazing plans because you put some real thought into how they can do a good job at it. That's not your job. Your job to is figure all that out, and then ruin for your NPCs.
Real people are messier than your perfect plans. They might have great-sounding plans, but they've also got obligations to a handful of other important (to them) people that divide their attention. They send someone else, someone less qualified, to do part of the work. They cut corners on expenses or dodge personal risks. They might have moral qualms about some of what they are doing, leading them to hesitate at the wrong time or deviate from the plan. They have ulterior motivates; schemes within schemes that make the whole system more fragile. There might be infighting in the secret society.
All of these flaws follow from the personalities and values of the characters involved. Make your NPCs care about things, have fears, and have foibles. Not only do these flaws cause them to err in plot-necessary ways, they humanize the characters. It adds dimension and believability.
Ripples Are Everywhere
Conspiracies don't exist in a vacuum. They have bills to pay, spaces they gather in, and people they work with. Even when outright errors don't happen, footprints are still left behind.
Paper trails and other bureaucratic evidence can used to feed a simple piece of information to the PCs. Doing the kind of research that yields this information is notoriously boring, so it's best to summarize what the PCs found. For example: “After you and your intern searched for two days, you discovered that Morgana Holding, LLC has been buying property for the past ten years. Curiously, Morgana's holdings have all remained un-rented and purportedly vacant. Plotting the properties on a map, you notice they form a perfect grid.”
Human contacts are another form of eviedence. They can deliver versatile information and are a great role-play opportunity. The toadies, employees, and casual contacts of the secret society's members are far more plausibly accessible. They are the ones who are don't have all of the information, but they know a few pieces. They don't always understand the gravity of the secrecy, often because they haven't been formally inducted to the society and don't know all of its practices.
These secondaries are just as prone to flaws as anyone else, so they have “cracks” all their own. Sometimes, the problems flow from the same place as the their ties to the conspiracy. For example, a ghoul servant who is subjected to frequent abuse will still be loyal to their master. However, they are emotionally damaged by their situation, and may reach out for help or solace in unexpected ways.
Ripples Bounce Back
As the PCs act, they will sometimes get noticed. Track what the NPCs might have learned about them, and how they might react. Each reaction should leave behind a new type of evidence, even reactions intended to cover one's tracks.
The Players Have To See Something
Always keep in mind that your players' only window into this world comes from what you tell them at the game table. You have to lead them towards some of the secrets eventually. Use scene descriptions to make important things stand out and feel interesting. Important things should usually be a blend of plot hooks and scene-setting flavor. How you adjust the balance between the two is a question of how much you need/want to drive plot quickly versus how important it is to evoke a mood for the roleplaying.
When I started GMing, I found it hard to let PCs find out secrets because I kept thinking of them as secret. This is stuff the players are supposed to find out. They should get bits of it in every session. Keep telling yourself that!