I don't know if I can link things from another FM web site? I'll give it a go and if its removed then I'll understand.
I was having the exact same problem as the OP,
how can my my top flight team be getting battered by a third tier club?
But then I read
this article about opposition instructions.
What I have done since is to stop my assistant manager auto applying OI's and I have created my own for each position.
I read how the person from said article^ neutralized opposition threats so I thought about creating general OI's to suit my tactic.
They are more rule of thumb OI's, just the basic things I want my team to do and to make pre-match setup faster.
Now there is probably no point me telling you all my OI's as they are for my tactic, my players etc but I do urge you the read the article.
P.s I am very new to FM (only playing game for about a year) and this will probably old news and basic stuff.
But since I applied my rule of thumb OI's I have been so dominant that I'm now looking at ways to keep players behind the ball and drop deeper because with 18 or so players in their 18 yard area I'm finding it hard to score...
P.p.s It has not stopped my multi million pound players making Sunday pub league passes though, sadly :'(