|Ut custódiant te in ómnibus viis tuis.||That they guard you in all your ways.|
This is the second half of the clause (see previous post).
custodiant = that they guard you. We are in the subjunctive mood here, from the infinitive custodire. We use the infinitive because it is an ut clause, expressing intention or purpose.
in omnibus viis tuis = in all your ways. The preposition in can take the ablative or the accusative. When joined with an ablative (as is the case here) it simply means in.