I was trying to translate this post and thought that I had worked out "sevseydin" to mean "if you loved"

sev-se-y-din = verb stem + conditional suffix + fusion consonant + past tense second person suffix

But I put it into WinMekMak to check it and this gave the suffixes the other way round:

sevdiysen
sev-di-y-se-n = verb stem + past tense suffix + fusion consonant + conditional suffix + 2nd person possessive suffix

Which is correct or does the order of the suffixes not matter in this case???

They are two different things:

sevseydin: if you had loved (narrative of "conditional tense", expresses unreality)
Burasını sevseydin tatile buraya gelirdik.
If you had loved this place we would have come here. (but you didnt love).

In winmekmak
Choose from upper list (green list): condition (-se) +
Choose from lower list (purple list): imperfect (-di)

As you see winmekmak is listing 9 simple tenses. The upper list includes five simple tenses and 4 additional tenses.
From the upper list if you choose only "conditional tense" (se): gitse, gitsen, gitsem, ... (if he goes, if you go, if I go,...)

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sevdiysen: if you have loved (past tense condition)
Burasını sevdiysen tatile buraya gelebiliriz.
If you have loved this place we can come here for holiday.

In winmekmak
Choose from upper list: past (di) +
Choose from lower list: conditional (-se)

I suggest to work on the upper list first. These are the basic tenses and then with the lower list you make compound tenses with these.

hmmmmm.......
I still haven't really seen the difference

I think I need a large beer then to look at it again :-S