I want to create a spell with two magic effects. One of the effects is affected by modifications in strenght by e.g. perks. The second effect (in this case a decrease of magic resistance) should be always the same, e.g. 50%, but when I use something that changes the magnitude of the spell, of course both magic effects are affected.
How can I set the magnitude of a magic effect to a fixed and unchangeable value?

When you create a magic effect, there is a box named "Magic Skill" , have you set this to None for your magic resistance effect.
According to the CK wiki this box does:

Magic Skill: Theskill associated with the effect. The skill can modify the Power, Duration, or Cost of the effect, and will accumulate Skill Uses from it

Set the magic skill of the spell effect to none and remove all of the keywords from that mgef