Online multiple sequence alignment with constraints
Answer

You can't. Clustal doesn't provide the options of setting the sort of restraints you would like. Multiple Sequence Alignment (MSA) is difficult to program and the authors of Clustal have been refining their algorithm for years. If it were perfect and completely robust they might be in a position to add more user tweaking, but at the moment you're stuck with those provided. 

Comparison matrices and forcing alignments

It may be worth while to mention how one can force particular correspondences in simpler pairwise alignments. This involves manipulation of the comparison matrix used to score the comparison. DNA comparison matrices may be very simple, scoring, say, 1 for a perfect AA, TT, GG, CC match and 0 for any mismatch. Protein comparison matrices are more complex, with the values for perfect matches dependent on rarity and unique function (e.g. In the PAM250 substitution matrix WW scores 17, whereas GG scores only 5) and the values for mismatches also varying markedly (e.g. ED scores 4, compared with 5 for EE; but EW scores –7). There are various matrices available, so implementations of the Smith Waterman and Needleman and Wunsch pairwise comparison algorithms generally allow you to specify your own.

Suppose you have biological information (not intrinsic in the algorithm) that makes you wish to force an alignment. For example, AAATAA sequences near the polyA tail of two mRNA 3'UTRs should align, but sometimes do not because other stretches of As give better scores. What you can do is replace the AAATAA by AAAZAA in each case, and then modify the scoring matrix so that ZZ scores very highly (e.g. 20) compared with AA. This will force the alignment, after which you can change the Zs back to Ts.

Multiple Sequence Alignments tend to to use position-specific dynamic scoring matrices. As the overall sequences align, the original scoring system is adjusted to reflect the frequency found at a particular position. (For example if a position is skewed to E in 90% if cases, EE will score more than at a position in which E is found only in 20% of cases). 

I'm not saying it would not be possible to change the initial Clustal matrix with Zs at a particular position, but I don't think this possibility is provided. (Anyway your situation is more complex.) Glancing at the Clustal Omega paper, I see that they allow, indeed encourage, you to build up alignments from previous profiles. If you managed to force the alignments of a few sequences and input the profile derived from that, you might get what you want. But I imagine that requires the command-line program from Dublin, rather than the EBI online version.