The best brush and settings for line art is a little subjective. The G-Pen and the Mapping Pen are pretty common line art pens for comics based on crowquill nibs used by many comics artists. But you aren't limited to those pens - it's up to you and whatever style you're trying to achieve.
The easiest organizational method for layers (for me anyway) is to group your layers in Layer Folders based on stages. For example, create a Layer Folder for rough sketches, another Layer Folder for line art, another Layer Folder for color art, and another Layer Folder for lettering.
There are several methods for coloring in the lines without going over. One way is to create a color flats layer.
First, use the Paint Bucket Fill tool without any area scaling. Fill in all of your shapes on a Color Layer Below the Line Art and don't worry about accidentally clicking on the Black Line Art. If you have a lot of open Line Art, you'll need to create a Layer and draw in the shape edges. I call that layer Scratch in the example below. Be sure to fill the gutter space with White.
Once all of the color is filled, you need to delete any accidental fills you did under the Line Art. Make a selection of the Black Line Art Layer (Layer>Selection From Layer>Create Selection)
and go to your Flat Color Layer and Clear the selection.
Use the Line Width Correction Tool set to a Thicken Width with the slider cranked up and paint the entire color layer.
The colors will thicken until they meet at the center.
If you're going to prepare your comic for print you need an underprinting below the Black Line art layer made up of 60% Cyan and 40% of both Magenta and Yellow. And it has to be choked a bit.
To do this, make another selection of the Black Line Art Layer and create a layer above your color file. Shrink the selection one pixel for every 100 pixels of resolution (if the resolution of your file is 350ppi, for example, you should shrink the selection by 3 pixels) and fill with the 60/40/40 gray (R 119 G 133 B 144).
If you're lettering, make a copy of your lettering layer and go to Balloon of the Sub Tool Detail Palette and click the Fill / No Line button. Rasterize this copied text layer and make the Layer Effect color White. This will remove the black line of the text balloons and leave just the fill behind which extends to the mid-point of the balloon line. Place this trapped Balloons Layer (called Fill in the example below) above the Final Colors Layer.
I've reduced the opacity of the Black Line Art Layer in the second picture to show the color underneath. And I removed the Black Line Art Layer in the third picture to show how the final Flats Color would look.
Now you can make selections from the flats layer and render your colors on a new layer above the flats layer. Simply click the Reference Icon while on the flats layer and use the Magic Wand with the Reference Layer selected as the layer to choose from. You can work on the rendering layer while using the magic wand and it will make selections from the flats layers. Create a shortcut to hide the marching ants of the selection so you don't have to see it while you work (View>Show Border).
Option two for coloring inside the lines is to use the Anti-Overflow option in the Sub Tool Detail Palette. When you turn that on and set your line art layer to Reference, you can color on a new color layer using the brush and it won't flow over the lines.
Manga Studio 4EX is the English version of Comic Studio while Manga Studio 5 EX is the English version of Clip Studio Paint. Celsys is the program developer while Smith Micro is the distributor of the English versions. Smith Micro has now gone with the CSP branding and done away with the Manga Studio branding. It made sense early on to maintain the Manga Studio branding despite having two different base programs simply because Smith Micro built a name on Manga Studio (and both programs are used to make comics) but when Celsys released the English version of CSP it became confusing and muddied the branding.
MS4EX and MS5EX (CSP now) are two different programs. CSP is much more illustrative providing a very good brush engine for painterly works. MS4EX is much more focused on producing black and white comics (although it does have limited color capabilities) but since Celsys has discontinued the development of Comic Studio (in favor of developing CSP) it's pretty much abandonned software. The features that make MS4 such a good program for making comics have now been brought into CSP. Some things are not similar yet. There are no layers of different resolutions in the same file in CSP, for example.
There's a lot going on in your post so let's try and tackle this one at a time.
Regarding the Wacom - have you tried going to File>Preferences>Tablet and switching to one of the other tablet services? I think there are 6 or 7 of them in Mac so you would have to go through each to see which one works.
Regarding upgrading to Clip Studio Paint 1.5.4 from Manga Studio 5 - have you tried downloading the trial version of CSP? Enter your serial number using the trial version of CSP 1.5.4. The trial is the full version and just requires a serial to unlock.
Regarding the files - What is the error message you receive when you try to open the file. What OS did you upgrade to?
There are so many settings that could be causing this. The easiest thing for you to do (without having to troubleshoot every possible setting) is to reset the tool to its initial settings. It's the pinwheel button next to the monkey wrench at the bottom of the Tool Property palette. Click that. If the problem persists it'll be time to troubleshoot the settings of the tool or the settings of the Monoprice tablet.
The tool property palette shows a preview of it changing colour, but when it's used it stays black. The layer is a colour layer. I've been trying to find out what might be causing it via Youtube videos, etc but to no avail. Unfortunately the documentation for CSP is pretty poor on this sort of thing.
OK, so basically if I have two layers or even selections, I'd like to be able to align the objects, either to center or to left, right, top or bottom. Like, if I have two circles of different size, I'd like to align them so the smaller one is centered within the larger one.
If this is the place to post feature requests for CSP, I have a request.
I really like the new animation feature introduced in in the last update, but unless I am missing something, there is no way to add a sound track at the moment, which would be really helpful for doing lip sync.
So my request would be the following:
The ability to import a sound track
The ability to hear the sound doing preview
The ability to export a movie with the soundtrack