I would suggest you mix the dyes you can purchase at Rockler and woodcraft.  Use an eye dropper with the Transtint dyes and have a notepad to keep track of what you are doing.  Work the color wheel --- opposites on the color wheel cancel each other out ---  too red, add green;  too green, add red.    You can even add these to already mixed stains.  Don't be afraid to experiment a little.  This will cost a little money to get enough dyes on hand to work the color wheel.

You can lightly sand after dying but you risk removing some of the dye in some areas.This can create an interesting effect or even fix some over enthusiastic color application.
Generally I pretreat or raise the grain with distilled water before staining, I then lightly sand with an Aluminum Oxide pad (generic 3M Scotch guard burgundy) dust off and spray top coat.
Because you have pretreated with Charles Neil's prestain blotch control which I understand is a sizing, it probably already lifted the grain somewhat and has sealed it from any more grain raising. Unless the directions on the CN prestain blotch control says otherwise I would lightly sand it before you apply your stain and you should have minimal if no grain raising. In my experience if I have grain raising after staining, prepping for my second coating (light sanding with pad) removes the nibs.
Tim

Hi

www.floorsanding-uk.com

Please see my published article here:

http://www.periodproperty.co.uk/ppuk_discovering_article_039.shtml

1. Finish sand to P240.
2. Water wash.
3. Sand raised grain with lubricated (stearated) P240 or P400 Silicon carbide.
4. Apply water stain, water black with walnut crystals and dash of ammonia or soda crystals for a light colour, for a dark colour you will need a brown (or mix red and yellow in proportion with the black) aniline dye as making a dark walnut crystal stain will give it some pigment affect and may go patchy.
5. Sand with worn P320 sanding sponge or P400 paper (don't burn the edges)
6. Apply shellac to fix water stain.
7. When dry apply finish of choice. Either nitro cellulose (NC), oil based poly, water based poly. One coat of shellac will be okay after an hour or two for use with even NC.

TIPS:

Cherry, other fruit woods (also Maple/Beech) have very fine, tight swirly grain that changes direction so areas that appear smooth, flat and plain coloured may actually contain grain structures (cf. "straws") that lie perpendicular or at a large angle to the surface and so will absorb much more stain/pigment and will so appear darker, creating the "patchy" effect. By water washing and flattening the raised grain you will reduce some of the 'furriness' which can accentuate this.

When using a water stain you will get a very clear, transparent colour that will enhance the contrast of the figure not reduce it. If you use a shade or two lighter water stain, when dry you can add a small amount of spirit dye and/or pigment to the shellac, when applied with a squirrel or zorino colouring/polishing mop (brush) over two coats this will darken the initial stain to the required colour. The advantage of using this method is that whilst the water staining retains maximum clarity, the additional coats of shellac stain (which also fix, seal and apply body) add a semi opaque layer that helps to even up the patchy effect as the shellac colour will partly be absorbed and partly rest on the surface. If you require more evenness apply more coats of shellac or increase the amount of added spirit stain/pigment, if you require more clarity but permit more patchiness then apply/add less.

There is no magic way to eliminate patchiness as you cannot change the orientation of the wood fibres, you either use clear stain or pigment, accentuate or cover up. Using the above method you can very finely vary the amount of 'covering up' by getting most of the colour depth (shade) via clear water staining thus leaving you to apply a much smaller amount of pigmented stain (covering up)

I use this method al the time, frequently I will use three, four, five or more layers to build up an even and totally natural looking effect. The only caveat is that if you use more than two thin coats of shellac you may lose adhesion or cause bleeding/pulling issues with solvent based NC based lacquers. Shelac is actually an excellent barrier seal and very neutral, the key to goo adhesion is if you require strong mechanical strength to your finish do not sand the shellac layers, the slight grain raising will form little 'micro spikes' that will interleave with the top lacquer/finish. If you are finishing with shellac or wax then denibbing with P240/320/400 is fine.

Toby