Both are fine, although "be both preserved" is an archaic word order that it not generally seen in current usage - use "both be preserved" instead.
Otherwise, there is a slight semantic difference between the two, but it is so slight that in practice no-one would think of it.
It is important that they both be preserved.
This is using the subjunctive, and is theoretically not saying whether or not they are currently being preserved. It simply stresses that preservation is important.
It is important that they are both preserved.
Strictly speaking, this is saying that they are being preserved, and that it is important that this be so. If you're being really strict about the use of the indicative, you wouldn't use that if there's no preservation going on at the moment. However, that indicative/subjunctive distinction is entirely ignored in practice. People will frequently use the indicative in such situations when intending a subjunctive meaning. Thus, it cannot be said to be wrong to use it where the preservation is not currently taking place.
So, you say "shouldn't it be ...", and the answer is "yes and no". Yes, if you are trying to apply English grammar analytically and ignoring how people actually use the language. No, if you want to learn English how native speakers use it. There's no reason it should be that instead - but it can be, if you prefer it.