I tend to "circle around" to figure out the specs. First I'd write down the number answers to these questions:
1) What is the max output of my alternator in amps?
2) If I'm planning to self jump-start through the same wire, what is the amp draw of the starter (discounting inrush current)?
3) What is the maximum voltage drop I want to see? (For this figure, both wire size AND round trip length of run count.)
Then I guess/choose a wire size and run the calculations for voltage drop and check the ampacity tables to see if I can fuse high enough for the draws. If there is either too much voltage drop for question three, OR the ampacity charts won't allow me to fuse it high enough for the answers to the first two questions, then I go up a size and try again (with the calculations). When I get to a wire size that fits both, that's the one I use. For me, in DC systems, it's usually voltage drop that drives an up-size (especially for solar and/or electronics), but sometimes it is fusing (such as in the case of self jump-starting).
As was mentioned above, the protection (fuse/breaker) is typically sized based on the wire (size, temp rating, location, bundled or not, etc.). You are protecting the wire (and thus you and your rig) from shorts. (Sometimes you can fuse once for two things, but typically you fuse trunk wires for their capacity, and then if you need to protect appliances, etc. you do that further down the line with a fuse block or in-line fuse. The ampacity charts will go into more detail as to how large you can fuse a particular wire size. ABYC (boating advisory organization) has standards for many handy things (electrical, fuel, water, etc.) and publishes ampacity tables.
One note is that smaller fuses can make for more voltage drop than larger ones, so if you are, say, fusing your 15 amp solar system 2AWG down wire, don't fuse it for 20 amps, but rather something more like 90 amps (for the wire). (I realize that's not what you are doing in this case though.)
If you have the height, and if you don't have more than 10,000 amps of short circuit current in your battery bank* (unlikely in start bank, but very possible in house bank if it is more than around 250 amp hours), then I like the MRBF's. Because they sit right on the battery post, there is no unprotected wire (that would normally be between the battery and the fuse/breaker).
*This has to do with AIC rating, which can be an important factor in choosing a main fuse that is on a wire coming from a battery bank. AIC is "ampere interrupt capacity." Essentially this is not a rating for the fuse "blow" but rather for the strength of the fuse holder and the body of the fuse. The fuse (or breaker) will not do you any good if the body blows apart or the fuse melts together before it can blow.
An example:
My house bank consists of three Group 31 Lifeline batteries. They have 375 amp hours of storage capacity. To find out what AIC rating I need my fuse type to have, I need to see what the short circuit rating of the batteries is. That's because if there is a short in one of the battery cables, it's not 375 amps that will come out, but rather MUCH MORE power that is stored that can come blasting out. I look on Lifeline's chart and see that each of my batteries has a short circuit rating of 4,257 amps. So with three of them in my house bank, I have a potential of over 12,000 amps (12,771). I look up the MBRF fuses (which I do like) and see that they are rated at 10,000 amps (10,000 amps AIC rating). So I can't use one of those on my house bank. Instead, I go to a Class T fuse, which is rated at 20,000 amps AIC. I do, however, have an MRBF on my start bank, which has less than 5,000 amps short circuit rating. Even though one wire runs right from my house bank to my start bank, since I have the Class T on the house bank, there is no problem having an MRBF on the other end. Once I'm "downstream" of the Class T, I have already satisfied the AIC rating for the house bank and so the fuses after that don't all need to be Class T's.
I hope this wasn't too much information (?)
Vanaroo