Never invested in a BES before, but looking at one at the moment.
Before you worry too much about the mechanics of the transaction, are you sure it's the correct investment for you.
You are putting your investment into a single company. It is a start up company so has no track record and little penetration into the market it's aiming at. The track record for start up companies isn't that healthy, worth looking up the stats if you can find them online. The stats for the BES companies also isn't that healthy, again, have an idea of just how many of the companies crash and burn.
The upside, you get great tax breaks and if the company does well......
Do plenty of homework before investing.
(open to correction on all figures)
You've already paid the tax on the money, so my view would have been you provide a certain amount, the goverment pays the tax which would originally have been paid.
I.e. you want to invest X, the gov tops this up with the original tax which you paid on X so your investment is 0.52X + the gov's contribution of 0.48X.
Never dealt with the BES system so very open to being corrected here.