Yes, a wrapper is needed for Glide64. You put the file "glide3x.dll" in the SAME DIRECTORY AS YOUR EMULATOR. So whichever folder Project64.exe is, put that glide3x.dll in the same directory. Should work fine if you do that.
Obviously, even the wrappers themselves aren't 100% perfect yet. They're getting there though. I think the wrapper that comes with the Napalm WX release is what is causing the background/3D model priority issue in RE2 64. However, there is no better wrapper at the moment. It's the fastest and most compatible at this time.
And the other files (glide64.dll, glideHQ.dll, and even sometimes glide64.ini) goes in your graphics plugin directory (you know, with the rest of your plugins).
It might get confusing, but it really is the best plugin and worth the extra trouble for. One of my favorite things is that you can check specific compatibility settings for individual games, in the plugin. Better than having to go into the options for every game every time you load a new game! Here are some examples of things it can do that other plugins can't-
Banjo Kazooie- this game WAS pretty perfect on Jabo's plugin, but i find the glide64 plugin can emulate some effects faster. The jigsaw effect when entering a level can be emulated by checking "read every frame" in the plugin options.
Banjo Tooie- supports full hardware framebuffer effects used for the pause screen and the jiggy puzzle screen. I also think the shadows are transparent in glide, whereas they're opaque and black in Jabo, not sure.
Donkey Kong 64- with "read every frame" checked in the plugin settings, it can emulate almost every single effect that other plugins can't. This includes the blurred pause menu, the bananaport zipper transition, and even some extra zipper/transition effects. Also supports some fading and transparency effects on certain objects (such as the non-activated bananaports, the pop-in when you get close to enemies, and even some activated switches). Polygons DO stick out of the characters at times, and when climbing trees it's possible to get stuck and have a glitch which resets the level, but those are the emulator's fault and we'll have to wait for an update on that. I'd recommend occasional savestates in case.
Conker's Bad Fur Day- Supports very accurate hardware framebuffer emulation to make the pause menu appear correctly (blurs the current screen as it's supposed to, not a garbled mess). I would assume the matrix effect works too, not gotten that far though. Everything here looks pretty much perfect from what i've seen. I've not played the original much though. Might want to tick "read every frame" if you spot something I missed, usually fixes everything, but is slower.
Resident Evil 2- best thing here is that glide64 support the full motion videos, something Jabo's can't do, and it's awesome! Good support for the hardware framebuffer effects. Apart from the background priorities, the game is pretty much perfect, even the voices work with the right emulator settings.
Paper Mario- this is probably my favorite improvement over jabo's plugin. Using glide, the game is 99% perfect from what i've seen. The graphics don't flash and induce seizures (like Jabo's), the enemy encounter transition works great, and even small details like Bowser's fire breath and background candles look correct. This game had a ton of trouble on other plugins, glide though works epically! "read every frame" is slow, but thankfully not required for this game.
Super Mario 64- last but not least, this game always had issues emulating certain pixellated fading effects such as the invisibility cap, Bowser fading, and even the warp effects. Then you have the infamous painting of Peach which fades into Bowser as you run towards it. All those effects are perfectly emulated here, and the game is now what i'd consider as "flawless". I've seen no glitches so far whatsoever. Awesome work here.
So, long post is long. If you have a fast computer, N64 emulation is now better than ever with PJ64 and Glide64. Just make sure you DO have a decent computer, even without filtering the emulation can get slow with "read every frame" checked (which fixes most problems in games). As long as you have a good recent processor, you should be good.
By the way, there's a guy named Orleans who compiles and uploads the latest SVN's of Glide64's current development. Here's his uploads-
http://cid-ec92aae47a89073b.skydrive.live....64?view=details
He even uploads other emulators such as Dolphin, he updates daily, probably even hourly. If you don't mind the risk of trying something very WIP, you could try these. They're quite more up to date than the Glide64's on the official site, in fact there was a new version compiled today.