Well, let's set things straight!
1. Make sure that every engine you installed works on 1 thread, low priority, 128 hash size minimum and TBs assigned to each engine - names given, for example, Houdini 3_1, Houdini 3_2 and so on. Low priority is needed so you can use all your 6 cores of your computer without having problems to work whatever you wish while analysing with the Aquarium's IDeA.
2. Make sure you have a root assigned on the desired move correctly. With 6 cores you can assign at least 5 more roots wherever you like on some promising lines. For example, if you want to analyse the starting chess position when you're the first player, the basic root is at the very start. And if you are planning to play 1.e4, then you can place the second root after 1...e5, the third one after 1....c5, the fourth - after 1.e4 e5 2.Nf3 Nc6 3.Bb5 a6 4.Ba4 Nf6 5.0-0 Be7 6.Re1 b5 7.Bb3, the fifth after 1.e4 c5 2.Nf3 d6 3.d4 cxd4 4.Nxd4 Nf6 5.Nc3 a6 ....and so on..
You can change these roots whenever you like while analysing - the software starts to use them on the next alternatives / promising lines stage. If you have 6 roots, every engine will take one root and will start generating moves from this root further.
3. First make infinite analysis with different engines (great depth is not needed) - no matter which software you like to use, write the results in a pgn-file, paste it in the so-called "Sandbox" in the Aquarium. Make the IDeA-project from there, making sure your mouse cursor is on the right move that will be the first root of the project. Return to the Sandbox, copy all the moves after the root move and paste it into the IDeA project that you've just created. Start the project and press the button "All positions", thus giving all the moves to the IDeA as tasks to analyse. It will save you time, because the IDeA will start on the right paths at once. And of course, it will make alternatives for every move of your lines.
4. Making a project is better to start as 'default', leaving it at least for a night. 30secs AND 21 plies (maximum 40 seconds) does the job usually. Endgames may need 60 secs OR 30 plys.. Tactical positions may need the 'aggressive' option instead of the "default" one (and don't forget to make your Houdini 3 engines "tactical"). I use 35 to 40 per cents "tree width" most of the times.
5. Next stage is to prolong the analysis changing the "default" option to "longest", while limiting white and black alternatives to 10, 8 or 6 depending on the position you analyse. It can be done "on the fly" also, as almost everything in this software.
6. You can use every option you see in the GUI as you like - my numbers here are as an example. Some users have completely different styles to extract results from this powerful tool. For example, 15 secs AND 15 plys, "wider" tree, then "default", then "longest" for most of the positions.
7. Do not forget that this tool is 'Interactive' - you have to follow lines and stepping on a move you can press on "current position" or "alternative" buttons, as well as input interesting moves and lines manually moving the pieces directly on the chess board and pressing "current position" button. This way you can direct your analysis on the needed path. It's absolutely necessary, otherwise you'll have to wait for till the Kingdom Come. Of course, there is a way to let the software do the job itself - "wider" option, 75 per cents tree shape and so on... But then the time will be not on your side..