So me and almost everyone I play with, even when multi-classing write out our xp as, 1000, 10000, 50000 (ect) as its accumulated. But one to two players who are not in the majority of our games. Being when the two groups overlap or combine for a adventure or two.Some of them write XP out separate for example 1500/1000 when multi-classing. Does this really make any difference? I mean in the end your XP total should add up the same and as I understand it a lv3 human rogue would still need the xp from level 3 to 4 to pick up another class for example lv1 swashbuckler. Am i misunderstanding something or is it that some players just separate things for whatever reason (these players started in 2ed so it might be a old habit)
You're correct that a Rogue 3 needs 3000 XP to level up, regardless of whether he uses that level to become a Rogue 4 or a Rogue 3/Swashbuckler 1. I suspect that this is a holdover from 2nd edition, because that's where I've seen it written this way before.
The only way that I think it would only matter is that it could be a cause for confusion if they do anything that could reduce their XP, which usually means casting spells with an XP cost or using any of the Item Creation feats - i.e., it might lead them to think that they have to choose which class to spend the XP from, when in fact there's no such thing.
Some of them write XP out separate for example 1500/1000 when multi-classing. Does this really make any difference?
No, the manner of recording XP doesn't change the total, which is all that really matters to a 3.5 character.
I mean in the end your XP total should add up the same and as I understand it a lv3 human rogue would still need the xp from level 3 to 4 to pick up another class for example lv1 swashbuckler.
No, somewhat surprisingly. It is true that you need a particular value of character (that is, not class specific) experience to get to the next level. However, in some circumstances you could be subject to an XP penalty. This means,for example, the 5,000 XP needed to get from level 5 (10k) to level 6 (15k) might actually be 6,250 XP earned while under a 20% penalty.
That is, the problem is two characters adventuring together surmounting the exact same obstacles can end up different levels, with different experience counts. It appears this accounting method is a way to rectify the possible difference.
Check out the section XP For Multiclass Characters on PHB 60. It details the process for multiclassing with different levels, including a possible* penalty. In particular, if you level your classes unevenly, there's a 20% penalty in XP gain. That is, leveling your fighter/wizard as ftr2/+wiz3/+ftr1 has no XP penalty, because the two classes were always within 1 level of each other. Leveling ftr3/+wiz3 would penalize XP gain for character level 4, when he's a ftr3/wiz1.
From there, you hit an odd patch every few levels where the multi-class character is actually a level behind (due to slower XP gain) the single-class companion. This also impacts experience gain, because the calculation for XP gain (DMG 36-37) is based on each distinct character's level. While this helps the lower level character catch up, it exacerbates the accounting problems.
As such, it seems like a good bookkeeping practice to count the classes separately when multiclassed, particularly if you aren't keeping the levels even.
In summary, this approach simply gives you the ability to compare your experience totals with a party mate's and have a clear delineation as to where each parts of the characters' XP actually came from.
As a final note, XP differences between party members can have a variety of other causes. These include, but aren't limited to, RP bonuses, spell costs, item crafting costs, and missing encounters. However, none of those are directly related to multiclassing, so I've ignored them for the bulk of this answer.
* It's possible to avoid this penalty either by keeping your class levels within 1 of each other, or by using the Favored Class noted in your race section.