Well, basically you'd like OS3.9, OS4.1, MorphOS for PuP and Work partitions.
I have gone the Debian PPC (Sarge) path and trust me... it wasn't for the faint hearted. Honestly it's one of the worst things I have done to my A1200D PPC cause it took me a whole weekend to setup since no official guide exists and what's worse... most repositories and paths from files that some guides link to, are either dead or changed over the years.
For A4000 it might be easier, but on A1200 that ONLY specific PCMCIA Ethernet NICs are compatible with (none of the 3COM and very rarely seen on eBay), you're pretty much screwed cause you'll certainly need an network access for ease of installation...
Anywayz... Linux installation needs actually 1 partition and 1 swap. The bootstrap command can run from your existing 3.9 installation UNLESS you want another light 3.1 installation to start the bootstrap automaticaly like booting to Linux at once (by Early Startup Menu)
Apart from Linux now...
- OS3.9 -->
I never needed more than 950MB (wanted a bit under the 1GB space for safety reasons) of 3.9 space (including all my progs etc under System partition - for easier backup procedures). Seriously now... It's the system you'll spend your 95% of your Amiga time (trust me on this lol)
- OS4.1 -->
Since I never messed a lot with OS4.x I kept an 950MB partition as well for the system and programs (dunno if it's ok nowadays but I guess I'll go with that number as well when I'll setup 4.1 on my miggy for means of completeness. You might actually need an SWAP partition in case you Amiga has <=128MB of RAM. For >=256MB the SWAP partition is not needed.
- MorphOS -->
I kept again an 950MB partition for that drive as well along with programs etc. Lack of registering MorphOS nowadays is a serious Thumbs-Down for me, not because I need to restart every once and a while, but because I really hate software with restrictions (I buy most of stuff that I use anyway).
- Work -->
This is your main partition for your Data, although you can have more partitions based on your need (like GAMES, DEMOS, MUSIC, blah blah). I thought that I didn't like that aspect cause I didn't want to have boundaries on my data. Just a simple GAMES, DEMOS, MUSIC folder was just fine under Work.
You can actually have folders like OS3.x, OS4.x, MOS etc to categorize which data is being used by every Operating System or have different Work partitions for every System (not so pretty imho though).
Make sure that if you make a huge Work partition you need to have some patched SCSI.device and a filesystem that supports big Hard Disks. (PFS3 which is the best FS imho has a restriction of 127GB afaik so either split your partitions of check for other FS).
Also you can have an FAT partition in case you wanna install all the above AmigaOSes plus Linux to have a common partition for exchanging data.
That's all I guess
People have different opinions on these matters, but I'm just expressing my personal taste etc.