Hi PanTheMan!
Merry Christmas to you first of all.
beyond that.....
in answer to question 1 - i would suggest you check out how you have set up your HardDrives on winuae. i know it's possible to 'lock out' HD write-access... maybe you have done this, and it's just a check-box you need to tick/untick (i admist i havent used winuae for a long time, so i'm not sure)
question 2 - this is one of the most open-ended questions i've ever seen on this forum!! it very much depends pn how you want to approach the management end of your game.
I am not saying that this is what you "should" do, but this is how i would approach such a game:
i would look at putting in place a timer, to regulate your 90 minutes (plus extras) first of all. do you want 90 minutes to be displayed across a genuine 90mins, or across 3 minutes?
you then have a BIG decision to make; "real" style activities (where the ball can be tracked across the whole "90 mins") or do you want your game to just follow the "major" events of the match? (goals, free-kicks, bookings, sending-offs, etc)
the above will massively affect how you program the rest of the game/match.
after that, it's a matter of generating random / seeded events depending on how you want the game to play out. You weigh randoms decisions in-favour/against certain outcomes, depending on player/team skill and/or abilities (depending on how much data you wish to track), home/away advantage, genuine 'random factor' , (and probably other aspects i cant think of right now!) , ..... from using this you can generate info on how your game "plays out"... maybe you can include such factors as having a good half-time team talk inspiring your players (all you need to do is weigh the random factors in the team's favour afterwards) - or perhaps multiple scorings (such as going 3-0 down) "un-inspires" a team to potentially concede more goals.....
at this stage the game is really left as open as you want it to be... there are many elements to consider!
I am sorry if my comments seem to cut-short, but you havent really picked the best time (i've just got in from the pub after xmas eve!) but i also hope it's given you enough to think-about/consider! I have played a lot of "SWOS" (sensi world of soccer) in my time, although, not so much pure-management-sims, but i hope it's enough to help you out for now!!
good luck, and please let me know what you think of the comments so-far, and i'll be happy to provide more